diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index c2c7b3f..39b923c 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -6,7 +6,7 @@ jobs: strategy: matrix: os: [ubuntu-latest, macos-latest] - python-version: ["3.10", "3.11"] + python-version: ["3.11"] name: Python ${{ matrix.python-version }} (${{ matrix.os }}) steps: - uses: actions/checkout@v3 @@ -16,11 +16,9 @@ jobs: python-version: ${{ matrix.python-version }} - name: Install dependencies run: | - python -m pip install pytest - python -m pip install . - git clone https://github.com/pha4ge/primer-schemes.git + python -m pip install '.[dev]' - name: Test with pytest + env: + PRIMASCHEMA_ROOT_PATH: ${{ github.workspace }} run: | pytest - env: - PRIMER_SCHEMES_PATH: "${{ github.workspace }}/primer-schemes" diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index ec7f5d3..5707941 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,11 +1,7 @@ repos: -- repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.2.0 - hooks: - - id: check-yaml - - id: end-of-file-fixer - - id: trailing-whitespace -- repo: https://github.com/psf/black - rev: 22.3.0 - hooks: - - id: black +- repo: https://github.com/astral-sh/ruff-pre-commit + rev: v0.4.4 + hooks: + - id: ruff + args: [ --fix ] + - id: ruff-format diff --git a/README.md b/README.md index d25adc5..66ea4fd 100644 --- a/README.md +++ b/README.md @@ -2,13 +2,14 @@ # Primaschema -The toolkit for validating and building tiling amplicon PCR primer scheme definitions for inclusion in the [PHA4GE primer-schemes repository](https://github.com/pha4ge/primer-schemes), using 6 or 7 column Primal Scheme-like BED files and scheme metadata contained in a YAML file. +**🚨 Migration to v1 scheme specification in progress** +A toolkit for fetching, validating and interrogating tiled amplicon PCR primer scheme definitions. Provides convenient programmatic accesss to the [PHA4GE primer-schemes repository](https://github.com/pha4ge/primer-schemes), a community repository of tiled amplicons primer schemes. -## Install (Python 3.10+) +## Install (Python 3.8+) -``` +```shell # Latest stable release pip install primaschema @@ -19,13 +20,14 @@ pip install ./primaschema # Development git clone https://github.com/pha4ge/primaschema.git cd primaschema -pip install --editable ./ +pip install --editable '.[dev]' +pre-commit install pytest ``` Some Primaschema commands use components from the [primer-schemes](https://github.com/pha4ge/primer-schemes) repository. To show Primaschema where to find these, create the environment variable `PRIMER_SCHEMES_PATH` pointing to the location of the primer-schemes directory on your machine: -``` +```shell git clone https://github.com/pha4ge/primer-schemes.git export PRIMER_SCHEMES_PATH="/path/to/primer-schemes" ``` @@ -35,32 +37,28 @@ export PRIMER_SCHEMES_PATH="/path/to/primer-schemes" ## Usage ``` -% primaschema --help +% primaschema -h usage: primaschema [-h] [--version] - {hash-ref,hash-bed,validate,validate-recursive,build,build-recursive,build-manifest,diff,6to7,7to6,show-non-ref-alts} - ... + {validate,build,build-manifest,hash-ref,hash-bed,diff,6to7,7to6,plot,show-intervals,show-discordant-primers,subset,sync} ... positional arguments: - {hash-ref,hash-bed,validate,validate-recursive,build,build-recursive,build-manifest,diff,6to7,7to6,show-non-ref-alts} + {validate,build,build-manifest,hash-ref,hash-bed,diff,6to7,7to6,plot,show-intervals,show-discordant-primers,subset,sync} + validate Validate one or more primer scheme definitions comprising info.yml, primer.bed and reference.fasta + build Build one or more primer scheme definitions comprising info.yml, primer.bed and reference.fasta + build-manifest Build a complete manifest of schemes contained in the specified directory hash-ref Generate reference sequence checksum hash-bed Generate a bed file checksum - validate Validate a primer scheme bundle containing info.yml, primer.bed and reference.fasta - validate-recursive Recursively validate primer scheme bundles in the specified directory - build Build a primer scheme bundle containing info.yml, primer.bed and reference.fasta - build-recursive Recursively build primer scheme bundles in the specified directory - build-manifest Build a complete manifest of schemes contained in the specified directory diff Show the symmetric difference of records in two bed files - 6to7 Convert a 6 column scheme.bed file to a 7 column primer.bed file using a reference sequence - 7to6 Convert a 7 column primer.bed file to a 6 column scheme.bed file by droppign a column - show-non-ref-alts Show primer records with sequences not matching the reference sequence + 6to7 Convert a 6 column scheme.bed file to a 7 column primer.bed file using reference backfill + 7to6 Convert a 7 column primer.bed file to a 6 column scheme.bed file by removing a column + plot Plot amplicon and primer coords from 7 column primer.bed + show-intervals Show amplicon start and end coordinates given a BED file of primer coordinates + show-discordant-primers + Show primer records with sequences not matching the reference sequence + subset Extract a primer.bed and reference.fasta scheme subset for a single chromosome + sync Retrieve/update local copy of remote primer scheme repository options: -h, --help show this help message and exit --version show program's version number and exit - - -% primaschema build test/data/primer-schemes/eden/v1 -INFO: Scheme bed file has the expected number of columns (6) -INFO: Writing info.yml with checksums -INFO: Generating primer.bed from scheme.bed and reference.fasta ``` diff --git a/pyproject.toml b/pyproject.toml index 3e0ac59..a8f97e3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,20 +1,21 @@ [build-system] -requires = [ - "setuptools >= 64", - "wheel >= 0.37.1", -] -build-backend = "setuptools.build_meta" +requires = ["flit_core >=3.2,<4"] +build-backend = "flit_core.buildapi" [project] name = "primaschema" -description = "A toolkit for primer scheme defintions" +authors = [ + {name = "Bede Constantinides", email="bedeabc@gmail.com"}, + {name = "Peter van Heusden", email="pvh@sanbi.ac.za"} +] +dynamic = ["version", "description"] readme = "README.md" -requires-python = ">=3.10" +requires-python = ">=3.8" keywords = ["genomics"] license = {text = "MIT License"} classifiers = [ "Framework :: Django", - "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.12", "Environment :: Console", "Intended Audience :: Science/Research", "License :: OSI Approved :: MIT License", @@ -23,21 +24,33 @@ classifiers = [ "Operating System :: MacOS", ] dependencies = [ - "biopython == 1.80", - "defopt == 6.4.0", - "pandas >= 1.5.3", - "pre-commit", - "pytest", + "altair>=5.3.0", + "biopython>=1.80", + "defopt==6.4.0", + "httpx>=0.27.0", "jsonschema", - "pyyaml", - "linkml==1.5.2", + "linkml", + "natsort>=8.4.0", + "pandas>=1.5.3", + "platformdirs>=4.2.2", + "pydantic>=2.0.0", + "pyyaml>=6.0.2", + "vl-convert-python>=1.6.0" ] -dynamic = ["version"] + [project.scripts] primaschema = "primaschema.cli:main" -[tool.setuptools.dynamic] -version = {attr = "primaschema.__version__"} +[project.urls] +Home = "https://github.com/pha4ge/primaschema" + +[project.optional-dependencies] +dev = [ + "pytest", + "pre-commit", + "flit" +] + +[tool.flit.external-data] +directory = "test" -[tool.setuptools.packages.find] -where = ["src"] diff --git a/src/primaschema/__init__.py b/src/primaschema/__init__.py index c8af519..dea8b1a 100644 --- a/src/primaschema/__init__.py +++ b/src/primaschema/__init__.py @@ -1,6 +1,64 @@ +"""Infrastructure for tiled amplicon PCR primer scheme definitions""" + +import logging +import logging.config +import os + from pathlib import Path -__version__ = "0.2.0" +from platformdirs import user_data_dir + + +__version__ = "1.0.0a0" + + +SCHEMES_ARCHIVE_URL = os.environ.get( + "PRIMASCHEMA_SCHEMES_ARCHIVE_URL", + "https://github.com/pha4ge/primer-schemes/archive/refs/heads/main.tar.gz", +) +CACHE_DIR = Path( + os.environ.get("PRIMASCHEMA_CACHE_DIR") or user_data_dir("primaschema", "PHA4GE") +) + +PKG_DIR = Path( + os.environ.get( + "PRIMASCHEMA_ROOT_PATH", Path(__file__).absolute().parent.parent.parent + ) +) +SCHEMA_DIR = PKG_DIR / "src" / "primaschema" / "schema" +MANIFEST_SCHEMA_PATH = SCHEMA_DIR / "manifest.json" +MANIFEST_HEADER_PATH = SCHEMA_DIR / "manifest-header.yml" + +logging_config = { + "version": 1, + "disable_existing_loggers": False, + "formatters": { + "default": { + "format": "%(name)s %(levelname)s: %(message)s", + }, + }, + "handlers": { + "console": { + "class": "logging.StreamHandler", + "formatter": "default", + "level": "INFO", + "stream": "ext://sys.stderr", + }, + }, + "root": { + "handlers": ["console"], + "level": "INFO", + }, + "loggers": { + "primaschema": { + "handlers": ["console"], + "level": "INFO", + "propagate": False, + }, + }, +} + +logging.config.dictConfig(logging_config) +logger = logging.getLogger("primaschema") -# pkg_dir = Path(__file__) -# data_dir = pkg_dir.parent / "data" +logger.debug(f"{PKG_DIR=} {SCHEMA_DIR=}") diff --git a/src/primaschema/cli.py b/src/primaschema/cli.py index 955c7d8..5d4d725 100644 --- a/src/primaschema/cli.py +++ b/src/primaschema/cli.py @@ -1,120 +1,148 @@ -import logging import sys +import logging + from pathlib import Path import defopt -import primaschema.lib as lib +from . import lib, logger -logging.basicConfig(format="%(levelname)s: %(message)s", level=logging.INFO) +def configure_logging(debug: bool): + if debug: + logger.setLevel(logging.DEBUG) + for handler in logger.handlers: + handler.setLevel(logging.DEBUG) + else: + logger.setLevel(logging.INFO) + for handler in logger.handlers: + handler.setLevel(logging.INFO) -def hash_bed(bed_path: Path): +def hash_bed(bed_path: Path, debug: bool = False): """ Generate a bed file checksum - :arg ref_path: Path of bed file + :arg bed_path: path of bed file + :arg debug: show debug messages """ + configure_logging(debug) hex_digest = lib.hash_bed(bed_path) print("BED checksum:", file=sys.stderr) print(hex_digest) -def hash_ref(ref_path: Path): +def hash_ref(ref_path: Path, debug: bool = False): """ Generate reference sequence checksum - :arg ref_path: Path of reference sequence + :arg ref_path: path of reference sequence + :arg debug: emit debug messages """ + configure_logging(debug) hex_digest = lib.hash_ref(ref_path) print("Reference checksum:", file=sys.stderr) print(hex_digest) -def validate(scheme_dir: Path): - """ - Validate a primer scheme bundle containing info.yml, primer.bed and reference.fasta - - :arg scheme_dir: Path of scheme.bed file - :arg out_dir: Path of directory in which to save primer.bed - :arg force: Overwrite existing output files - """ - return lib.validate(scheme_dir) - - -def validate_recursive(root_dir: Path, force: bool = False): - """ - Recursively validate primer scheme bundles in the specified directory - - :arg root_dir: Path in which to search for schemes - :arg force: Overwrite existing schemes and ignore hash check failures - """ - lib.validate_recursive(root_dir=root_dir, force=force) - - -def build(scheme_dir: Path, out_dir: Path = Path(), force: bool = False): - """ - Build a primer scheme bundle containing info.yml, primer.bed and reference.fasta - - :arg scheme_dir: Path of input scheme directory - :arg out_dir: Path of directory in which to save scheme - :arg force: Overwrite existing output files - """ - lib.build(scheme_dir=scheme_dir, out_dir=out_dir, force=force) - +def validate( + scheme_dir: Path, + full: bool = False, + ignore_checksums: bool = False, + recursive: bool = False, + rebuild: bool = False, + debug: bool = False, +): + """ + Validate one or more primer scheme definitions comprising info.yml, primer.bed and reference.fasta + + :arg scheme_dir: path of scheme.bed file + :arg full: perform meticulous validation using full model + :arg ignore_checksums: ignore checksum mismatches + :arg recursive: recursively find and validate primer scheme definitions + :arg rebuild: forcibly rebuild the pydantic model from the linkml model + :arg debug: show debug messages + """ + configure_logging(debug) + return lib.validate( + scheme_dir, + full=full, + ignore_checksums=ignore_checksums, + recursive=recursive, + rebuild=rebuild, + ) -def build_recursive(root_dir: Path, force: bool = False, nested: bool = False): - """ - Recursively build primer scheme bundles in the specified directory - :arg root_dir: Path in which to search for schemes - :arg force: Overwrite existing schemes and ignore hash check failures - :arg nested: Build definitions inside a nested dir structure of family/version - """ - lib.build_recursive(root_dir=root_dir, force=force, nested=nested) +def build( + scheme_dir: Path, + out_dir: Path = Path("built"), + nested: bool = False, + plot: bool = False, + recursive: bool = False, + ignore_checksums: bool = False, + debug: bool = False, +): + """ + Build one or more primer scheme definitions comprising info.yml, primer.bed and reference.fasta + + :arg scheme_dir: path of input scheme directory + :arg out_dir: path of directory in which to save scheme + :arg nested: use nested output structure ({organism}/{scheme_name}/{amplicon_length}/{version}) + :arg plot: plot primers in SVG format + :arg recursive: recursively find, validate and build primer scheme definitions + :arg ignore_checksums: ignore checksum mismatches + :arg debug: show debug messages + """ + configure_logging(debug) + lib.build( + scheme_dir=scheme_dir, + out_dir=out_dir, + nested=nested, + plot=plot, + recursive=recursive, + ignore_checksums=ignore_checksums, + ) -def build_manifest(root_dir: Path, schema_dir: Path = Path(), out_dir: Path = Path()): +def build_manifest(root_dir: Path, out_dir: Path = Path()): """ Build a complete manifest of schemes contained in the specified directory - :arg root_dir: Path in which to search for schemes - :arg schema_dir: Path of schema directory - :arg out_dir: Path of directory in which to save manifest + :arg root_dir: path in which to search for schemes + :arg out_dir: path of directory in which to save manifest """ - lib.build_manifest(root_dir=root_dir, schema_dir=schema_dir, out_dir=out_dir) + lib.build_manifest(root_dir=root_dir, out_dir=out_dir) -def seven_to_six(bed_path: Path, out_dir: Path = Path()): +def seven_to_six(bed_path: Path): """ - Convert a 7 column primer.bed file to a 6 column scheme.bed file by droppign a column + Convert a 7 column primer.bed file to a 6 column scheme.bed file by removing a column - :arg bed_path: Path of primer.bed file - :arg out_dir: Path of directory in which to save primer.bed + :arg bed_path: path of primer.bed file """ - lib.convert_primer_bed_to_scheme_bed(bed_path=bed_path, out_dir=out_dir) + bed_str = lib.convert_primer_bed_to_scheme_bed(bed_path=bed_path) + print(bed_str) -def six_to_seven(bed_path: Path, fasta_path: Path, out_dir: Path = Path()): +def six_to_seven(bed_path: Path, fasta_path: Path): """ - Convert a 6 column scheme.bed file to a 7 column primer.bed file using a reference sequence + Convert a 6 column scheme.bed file to a 7 column primer.bed file using reference backfill - :arg bed_path: Path of scheme.bed file - :arg fasta_path: Path of reference sequence - :arg out_dir: Path of directory in which to save primer.bed + :arg bed_path: path of scheme.bed file + :arg fasta_path: path of reference sequence """ - lib.convert_scheme_bed_to_primer_bed( - bed_path=bed_path, fasta_path=fasta_path, out_dir=out_dir + bed_str = lib.convert_scheme_bed_to_primer_bed( + bed_path=bed_path, fasta_path=fasta_path ) + print(bed_str) def diff(bed1_path: Path, bed2_path: Path, only_positions: bool = False): """ Show the symmetric difference of records in two bed files - :arg bed_path1: Path of first bed file - :arg bed_path2: Path of second bed file + :arg bed_path1: path of first bed file + :arg bed_path2: path of second bed file :arg only_positions: Use only primer positions when computing differences """ df = lib.diff(bed1_path, bed2_path, only_positions) @@ -122,22 +150,24 @@ def diff(bed1_path: Path, bed2_path: Path, only_positions: bool = False): print(df.to_string(index=False)) -def show_non_ref_alts(scheme_dir: Path): +def discordant_primers(scheme_dir: Path): """ Show primer records with sequences not matching the reference sequence - :arg scheme_dir: Path of input scheme directory + :arg scheme_dir: path of input scheme directory """ - print(lib.show_non_ref_alts(scheme_dir=scheme_dir)) + df = lib.discordant_primers(scheme_dir=scheme_dir) + if not df.empty: + print(df.to_string(index=False)) -def print_intervals(bed_path: Path): +def amplicon_intervals(bed_path: Path): """ - Print intervals covered by primers in a BED file + Show amplicon start and end coordinates given a BED file of primer coordinates - :arg ref_path: Path of bed file + :arg bed_path: path of bed file """ - all_intervals = lib.compute_intervals(bed_path) + all_intervals = lib.amplicon_intervals(bed_path) sorted_by_chrom = sorted(all_intervals.items()) for chrom, intervals in sorted_by_chrom: sorted_interval_keys = sorted(intervals, key=lambda x: (x[0], x[1])) @@ -146,21 +176,50 @@ def print_intervals(bed_path: Path): print(f"{chrom}\t{interval[0]}\t{interval[1]}\t{name}") +def subset(scheme_dir: Path, chrom: str, out_dir: Path = Path("built")): + """ + Extract a primer.bed and reference.fasta scheme subset for a single chromosome + + :arg scheme_dir: path of input scheme directory + :arg chrom: name of chromosome for which to generate a subset scheme definition + :arg out_dir: path of directory in which to save subset scheme + """ + lib.subset(scheme_dir=scheme_dir, chrom=chrom, out_dir=out_dir) + + +def synchronise(): + """ + Retrieve/update local copy of remote primer scheme repository + """ + lib.synchronise() + + +def plot(bed_path: Path, out_path: Path = Path("primer.html")): + """ + Plot amplicon and primer coords from 7 column primer.bed + + :arg bed_path: path of primer.bed file + :arg out_path: path of generated plot (with .html, .pdf, .png, or .svg extension) + """ + lib.plot_primers(bed_path=bed_path, out_path=out_path) + + def main(): defopt.run( { - "hash-ref": hash_ref, - "hash-bed": hash_bed, "validate": validate, - "validate-recursive": validate_recursive, "build": build, - "build-recursive": build_recursive, "build-manifest": build_manifest, + "hash-ref": hash_ref, + "hash-bed": hash_bed, "diff": diff, "6to7": six_to_seven, "7to6": seven_to_six, - "show-non-ref-alts": show_non_ref_alts, - "intervals": print_intervals, + "plot": plot, + "show-intervals": amplicon_intervals, + "show-discordant-primers": discordant_primers, + "subset": subset, + "sync": synchronise, }, no_negated_flags=True, strict_kwonly=False, diff --git a/src/primaschema/lib.py b/src/primaschema/lib.py index 9c83bb4..0dee06e 100644 --- a/src/primaschema/lib.py +++ b/src/primaschema/lib.py @@ -1,49 +1,48 @@ import hashlib -import json -import logging -import os import re import shutil import sys + from collections import defaultdict from pathlib import Path from tempfile import TemporaryDirectory -from typing import Literal +from typing import Literal, Optional, Dict, Tuple -import jsonschema -import pandas as pd +import linkml.validator import yaml -from Bio import SeqIO -from linkml.generators.pythongen import PythonGenerator -from linkml.validators import JsonSchemaDataValidator -from linkml_runtime.utils.schemaview import SchemaView +import altair as alt +import pandas as pd -SCHEME_BED_FIELDS = ["chrom", "chromStart", "chromEnd", "name", "poolName", "strand"] -PRIMER_BED_FIELDS = SCHEME_BED_FIELDS + ["sequence"] -POSITION_FIELDS = ["chromStart", "chromEnd"] +from Bio import SeqIO +from linkml.generators.pydanticgen import PydanticGenerator -def scan(path): - """Recursively yield DirEntry objects""" - for entry in os.scandir(path): - if entry.is_dir(follow_symlinks=False): - yield from scan(entry.path) - else: - yield entry +from . import ( + logger, + MANIFEST_HEADER_PATH, + CACHE_DIR, + SCHEMA_DIR, + SCHEMES_ARCHIVE_URL, +) +from .schema import bed, info +from . import util +import json -def get_primer_schemes_path(): - """Locate primer-schemes repo root using environment variable""" - env_var = "PRIMER_SCHEMES_PATH" - if ( - not env_var in os.environ - or not (Path(os.environ[env_var]).resolve() / "schema").exists() - ): - raise RuntimeError( - f'Invalid or unset environment variable {env_var} ({os.environ.get(env_var)}).\n\nSet {env_var} to the path of a local copy of the primer-schemes repo to proceed. For example, do `git clone https://github.com/pha4ge/primer-schemes` followed by `export {env_var}="/path/to/primer-schemes"`' - ) - return Path(os.environ[env_var]).resolve() + +SCHEME_BED_FIELDS = ["chrom", "chromStart", "chromEnd", "name", "poolName", "strand"] +PRIMER_BED_FIELDS = SCHEME_BED_FIELDS + ["sequence"] +HASHED_BED_FIELDS = [ + "chrom", + "chromStart", + "chromEnd", + "poolName", + "strand", + "sequence", +] +POSITION_FIELDS = ["chromStart", "chromEnd"] +MANDATORY_FILES = ("primer.bed", "reference.fasta", "info.yml") def hash_string(string: str) -> str: @@ -74,6 +73,7 @@ def parse_primer_bed(bed_path: Path) -> pd.DataFrame: return pd.read_csv( bed_path, sep="\t", + comment="#", names=PRIMER_BED_FIELDS, dtype=dict( chrom=str, @@ -87,41 +87,52 @@ def parse_primer_bed(bed_path: Path) -> pd.DataFrame: ) -def normalise_primer_bed_df(df: pd.DataFrame) -> pd.DataFrame: +def sort_primer_df(df: pd.DataFrame) -> pd.DataFrame: + df["amplicon_number"] = df["name"].apply(lambda x: int(x.split("_")[1])) + return df.sort_values( + [ + "chrom", + "amplicon_number", + "chromStart", + "chromEnd", + "poolName", + "strand", + "sequence", + ] + )[[*PRIMER_BED_FIELDS]] + + +def normalise_primer_df(df: pd.DataFrame) -> pd.DataFrame: """ - - Removes terminal whitespace - - Normalises case - - Sorts by chromStart, chromEnd, poolName, strand, sequence - - Removes duplicate records, collapsing alts with same coords if backfilled from ref + Removes terminal whitespace and normalises case + Sorts by chromStart, chromEnd, poolName, strand, sequence + Removes duplicate records, collapsing alts with same coords if backfilled from ref """ df["sequence"] = df["sequence"].str.strip().str.upper() - df = df.sort_values( - ["chromStart", "chromEnd", "poolName", "strand", "sequence"] - ).drop_duplicates() - return df + return sort_primer_df(df) -def hash_primer_bed_df(df: pd.DataFrame) -> str: +def hash_primer_df(df: pd.DataFrame) -> str: """ Returns prefixed SHA256 digest from stringified dataframe """ - string = df[["chromStart", "chromEnd", "poolName", "strand", "sequence"]].to_csv( - index=False - ) + normalised_df = normalise_primer_df(df) + string = normalised_df[[*HASHED_BED_FIELDS]].to_csv(index=False, header=False) + logger.debug(f"hash_primer_df() {string=}") return hash_string(string) def hash_primer_bed(bed_path: Path): """Hash a 7 column primer.bed file""" df = parse_primer_bed(bed_path) - return hash_primer_bed_df(df) + return hash_primer_df(df) def hash_scheme_bed(bed_path: Path, fasta_path: Path) -> str: """ Hash a 6 column scheme.bed file by first converting to 7 column primer.bed """ - logging.info(f"Hashing scheme.bed using reference backfill") + logger.info("Hashing scheme.bed using reference backfill") ref_record = SeqIO.read(fasta_path, "fasta") df = parse_scheme_bed(bed_path) records = df.to_dict("records") @@ -134,28 +145,29 @@ def hash_scheme_bed(bed_path: Path, fasta_path: Path) -> str: else: raise RuntimeError(f"Invalid strand for BED record {r}") bed7_df = pd.DataFrame(records) - return hash_primer_bed_df(bed7_df) + return hash_primer_df(bed7_df) -def convert_primer_bed_to_scheme_bed(bed_path: Path, out_dir: Path = Path()): +def convert_primer_bed_to_scheme_bed(bed_path: Path) -> str: df = parse_primer_bed(bed_path).drop("sequence", axis=1) - df.to_csv(Path(out_dir) / "scheme.bed", sep="\t", header=False, index=False) + return df.to_csv(sep="\t", header=False, index=False) -def convert_scheme_bed_to_primer_bed( - bed_path: Path, fasta_path: Path, out_dir: Path = Path() -): - ref_record = SeqIO.read(fasta_path, "fasta") +def convert_scheme_bed_to_primer_bed(bed_path: Path, fasta_path: Path) -> str: + ids_seqs = SeqIO.to_dict(SeqIO.parse(fasta_path, "fasta")) df = parse_scheme_bed(bed_path) records = df.to_dict("records") for r in records: + chrom = r["chrom"].partition(" ")[0] # Use chrom name before first space start_pos, end_pos = r["chromStart"], r["chromEnd"] if r["strand"] == "+": - r["sequence"] = str(ref_record.seq[start_pos:end_pos]) + r["sequence"] = str(ids_seqs[chrom].seq[start_pos:end_pos]) else: - r["sequence"] = str(ref_record.seq[start_pos:end_pos].reverse_complement()) + r["sequence"] = str( + ids_seqs[chrom].seq[start_pos:end_pos].reverse_complement() + ) df = pd.DataFrame(records) - df.to_csv(Path(out_dir) / "primer.bed", sep="\t", header=False, index=False) + return df.to_csv(sep="\t", header=False, index=False) def hash_bed(bed_path: Path) -> str: @@ -170,56 +182,79 @@ def hash_bed(bed_path: Path) -> str: def hash_ref(ref_path: Path): - record = SeqIO.read(ref_path, "fasta") - return hash_string(record.seq) + chroms_seqs = {} + for record in SeqIO.parse(ref_path, "fasta"): + chroms_seqs[record.id] = str(record.seq).upper() + chroms_seqs_sorted = {key: chroms_seqs[key] for key in sorted(chroms_seqs)} + string = "" + for chrom, seq in chroms_seqs_sorted.items(): + string += f">{chrom}\n{seq}\n" + logger.debug(f"hash_ref() {string=}") + return hash_string(string.strip()) def count_tsv_columns(bed_path: Path) -> int: - return len(pd.read_csv(bed_path, sep="\t").columns) + return len(pd.read_csv(bed_path, sep="\t", comment="#").columns) -def parse_yaml(path) -> dict: +def parse_yaml(path: Path) -> dict: with open(path, "r") as fh: return yaml.safe_load(fh) -def validate_yaml_with_json_schema(yaml_path: Path, schema_path: Path): - yaml_data = parse_yaml(yaml_path) - with open(schema_path, "r") as schema_fh: - schema = json.load(schema_fh) - return jsonschema.validate(yaml_data, schema=schema) - - -def validate_with_linkml_schema(yaml_path: Path, schema_path: Path): - schema_view = SchemaView(schema_path) - schema_gen = PythonGenerator(schema_view.schema) - schema_compiled = schema_gen.compile_module() - data = parse_yaml(yaml_path) - data_instance = schema_compiled.PrimerScheme(**data) - # print(yaml_dumper.dumps(data_instance)) - validator = JsonSchemaDataValidator(schema_view.schema) - validator.validate_object(data_instance) - - -def validate_bed(bed_path: Path, bed_type=Literal["primer", "scheme"]): - bed_columns = count_tsv_columns(bed_path) - if bed_type == "primer" and bed_columns != 7: - raise RuntimeError( - f"Primer bed files should have 7 columns: {PRIMER_BED_FIELDS}" - ) - elif bed_type == "scheme" and bed_columns != 6: - raise RuntimeError( - f"Scheme bed files should have 6 columns: {SCHEME_BED_FIELDS}" +def validate_scheme_yaml_with_linkml(path: Path) -> None: + data = parse_yaml(path) + report = linkml.validator.validate(data, SCHEMA_DIR / "info.yml", "PrimerScheme") + if report.results: + msg = "" + for result in report.results: + msg += f"{result.message}\n" + raise ValueError(msg) + + +def parse_scheme_yaml(path: Path) -> dict: + """Parse and validate with Pydantic""" + data = parse_yaml(path) + return info.PrimerScheme(**data).model_dump() + + +def validate_bed_and_ref( + bed_path: Path, ref_path: Optional[Path] = None +) -> bed.BedModel: + """Check that primer.bed is a tiled PrimalScheme v3 BED""" + with open(bed_path) as fh: + bed_contents = fh.readlines() + primers = [] + amplicons_primers = defaultdict(list) + for line in bed_contents: + if line.startswith("#"): + continue + r = line.split("\t") + primer = bed.PrimerModel( + chrom=r[0].partition(" ")[0], # We want to ignore anything after a space + chrom_start=int(r[1]), + chrom_end=int(r[2]), + name=r[3], + pool_name=int(r[4]), + strand=r[5], + sequence=r[6], ) + chrom = primer.chrom + amplicon_number = int(primer.name_parts[1]) + primers.append(primer) + amplicons_primers[(chrom, amplicon_number)].append(primer) + + amplicons = defaultdict(list) + for (chrom, amplicon_number), primers in amplicons_primers.items(): + amplicons[chrom].append(bed.AmpliconModel(primers=primers)) + + # If a ref_path is supplied, populate the reference_lengths field of BedModel + if ref_path: + records = SeqIO.parse(ref_path, "fasta") + reference_lengths = {r.id.partition(" ")[0]: len(r.seq) for r in records} else: - logging.info(f"Detected {bed_type} bed file with {bed_columns} columns") - - if bed_type == "primer": - hash_primer_bed(bed_path) - elif bed_type == "scheme": - hash_scheme_bed( - bed_path=bed_path, fasta_path=bed_path.parent / "reference.fasta" - ) + reference_lengths = None + return bed.BedModel(amplicons=amplicons, reference_lengths=reference_lengths) def infer_bed_type(bed_path: Path) -> str: @@ -235,165 +270,183 @@ def infer_bed_type(bed_path: Path) -> str: return bed_type -def validate(scheme_dir: Path, force: bool = False): - # schema_path = get_primer_schemes_path() / "schema/scheme_schema.latest.json" - logging.info(f"Validating {scheme_dir}") - validate_bed(scheme_dir / "primer.bed", bed_type="primer") - # validate_yaml_with_json_schema( - # yaml_path=scheme_dir / "info.yml", schema_path=schema_path - # ) - schema_path = get_primer_schemes_path() / "schema/primer_scheme.yml" - validate_with_linkml_schema( - yaml_path=scheme_dir / "info.yml", schema_path=schema_path - ) - scheme = parse_yaml(scheme_dir / "info.yml") - existing_primer_checksum = scheme.get("primer_checksum") - existing_reference_checksum = scheme.get("reference_checksum") - primer_checksum = hash_bed(scheme_dir / "primer.bed") - reference_checksum = hash_ref(scheme_dir / "reference.fasta") - if ( - existing_primer_checksum - and not primer_checksum == existing_primer_checksum - and not force - ): - raise RuntimeError( - f"Calculated and documented primer checksums do not match ({primer_checksum} and {existing_primer_checksum})" - ) - elif not primer_checksum == existing_primer_checksum: - logging.warning( - f"Calculated and documented primer checksums do not match ({primer_checksum} and {existing_primer_checksum})" - ) - if ( - existing_reference_checksum - and not reference_checksum == existing_reference_checksum - and not force - ): - raise RuntimeError( - f"Calculated and documented reference checksums do not match ({reference_checksum} and {existing_reference_checksum})" - ) - elif not reference_checksum == existing_reference_checksum: - logging.warning( - f"Calculated and documented reference checksums do not match ({reference_checksum} and {existing_reference_checksum})" - ) - logging.info(f"Validation successful for {scheme.get('name')} ") - +def validate( + scheme_dir: Path, + full: bool = False, + ignore_checksums: bool = False, + recursive: bool = False, + rebuild: bool = False, +) -> None: + info_schema_linkml_path = SCHEMA_DIR / "info.yml" + info_schema_pydantic_path = SCHEMA_DIR / "info.py" + if recursive: + for path in Path(scheme_dir).rglob("info.yml"): + if path.is_file() and path.name == "info.yml": + validate( + scheme_dir=path.parent, full=full, ignore_checksums=ignore_checksums + ) + else: + logger.info(f"Validating {scheme_dir}") + yml_path = Path(scheme_dir / "info.yml") + bed_path = Path(scheme_dir / "primer.bed") + ref_path = Path(scheme_dir / "reference.fasta") + + if ( + rebuild + or not info_schema_pydantic_path.exists() + or info_schema_pydantic_path.stat().st_size == 0 + ): + logger.info("Building intermediate pydantic model") + with open(info_schema_pydantic_path, "w") as fh: + fh.write(PydanticGenerator(info_schema_linkml_path).serialize()) + + if full: + logger.debug("Validating with linkml model") + validate_scheme_yaml_with_linkml(path=yml_path) + else: + logger.debug("Validating with pydantic model") + parse_scheme_yaml(yml_path) + + logger.debug("Validating primer.bed and reference.fasta") + validate_bed_and_ref(bed_path=bed_path, ref_path=ref_path) + + scheme = parse_scheme_yaml(yml_path) + existing_primer_checksum = scheme.get("primer_checksum") + existing_reference_checksum = scheme.get("reference_checksum") + primer_checksum = hash_bed(bed_path) + reference_checksum = hash_ref(ref_path) + if ( + existing_primer_checksum + and not primer_checksum == existing_primer_checksum + and not ignore_checksums + ): + raise RuntimeError( + f"Calculated and documented primer checksums do not match ({primer_checksum} and {existing_primer_checksum})" + ) + elif not primer_checksum == existing_primer_checksum: + logger.warning( + f"Calculated and documented primer checksums do not match ({primer_checksum} and {existing_primer_checksum})" + ) + if ( + existing_reference_checksum + and not reference_checksum == existing_reference_checksum + and not ignore_checksums + ): + raise RuntimeError( + f"Calculated and documented reference checksums do not match ({reference_checksum} and {existing_reference_checksum})" + ) + elif not reference_checksum == existing_reference_checksum: + logger.warning( + f"Calculated and documented reference checksums do not match ({reference_checksum} and {existing_reference_checksum})" + ) + logger.info(f"Validated {get_scheme_cname(scheme)}") -def validate_recursive(root_dir: Path, force: bool = False): - """Validate all schemes in a directory tree""" - schemes_paths = {} - for entry in scan(root_dir): - if entry.is_file() and entry.name == "info.yml": - scheme_dir = Path(entry.path).parent - scheme = scheme_dir.name - schemes_paths[scheme] = scheme_dir - for scheme, path in schemes_paths.items(): - validate(scheme_dir=path, force=force) +def format_primer_bed(bed_path: Path) -> str: + """Sort a primer bed into a maximally compatible format""" + df = parse_primer_bed(bed_path) + return sort_primer_df(df).to_csv(sep="\t", header=False, index=False) def build( - scheme_dir: Path, out_dir: Path = Path(), force: bool = False, nested: bool = True -): + scheme_dir: Path, + out_dir: Path = Path("built"), + plot: bool = False, + nested: bool = False, # Create nested output dir structure + recursive: bool = False, + ignore_checksums: bool = False, +) -> None: """ - Build a PHA4GE primer scheme bundle. - Given a directory path containing info.yml, reference.fasta, and either - primer.bed or reference.bed, generate a directory containing info.yml including - primer and reference checksums and a canonical primer.bed representation. + Validate and build a primer scheme given a scheme directory path. + Optionally do so recursively """ - validate(scheme_dir=scheme_dir, force=force) - scheme = parse_yaml(scheme_dir / "info.yml") - if nested: - family = Path(scheme["name"].partition("-")[0]) - version = Path(scheme["name"].partition("-")[2]) - out_dir = Path("built") / scheme["organism"] / family / version + if recursive: + for path in Path(scheme_dir).rglob("info.yml"): + if path.is_file() and path.name == "info.yml": + build( + scheme_dir=path.parent, + out_dir=out_dir, + plot=plot, + nested=True, + ignore_checksums=ignore_checksums, + ) else: - out_dir = Path("built") / scheme["name"] - try: - out_dir.mkdir(parents=True, exist_ok=force) - except FileExistsError: - raise FileExistsError(f"Output directory {out_dir} already exists") - scheme["primer_checksum"] = hash_bed(scheme_dir / "primer.bed") - scheme["reference_checksum"] = hash_ref(scheme_dir / "reference.fasta") - with open(out_dir / "info.yml", "w") as scheme_fh: - logging.info(f"Writing info.yml to {out_dir}/info.yml") - yaml.dump(scheme, scheme_fh, sort_keys=False) - logging.info(f"Copying primer.bed to {out_dir}/primer.bed") - shutil.copy(scheme_dir / "primer.bed", out_dir) - logging.info(f"Copying reference.fasta to {out_dir}/reference.fasta") - shutil.copy(scheme_dir / "reference.fasta", out_dir) - logging.info(f"Writing scheme.bed to {out_dir}/scheme.bed") - convert_primer_bed_to_scheme_bed(bed_path=out_dir / "primer.bed") - shutil.copy("scheme.bed", out_dir.resolve()) - os.remove("scheme.bed") - - -def build_recursive(root_dir: Path, force: bool = False, nested: bool = False): - """Build all schemes in a directory tree""" - schemes_paths = {} - for entry in scan(root_dir): - if entry.is_file() and entry.name == "info.yml": - scheme = parse_yaml(entry.path) - scheme_dir = Path(entry.path).parent - schemes_paths[scheme.get("name")] = scheme_dir - for scheme, path in schemes_paths.items(): - build(scheme_dir=path, force=force) - - -def build_manifest(root_dir: Path, schema_dir: Path, out_dir: Path = Path()): + validate(scheme_dir=scheme_dir, ignore_checksums=ignore_checksums) + scheme = parse_yaml(scheme_dir / "info.yml") + scheme_cname = get_scheme_cname(scheme) + if nested: + out_dir = Path(out_dir) / Path(scheme_cname) + else: + out_dir = Path(out_dir) / get_scheme_cname(scheme, sep="_") + try: + out_dir.mkdir(parents=True, exist_ok=True) + except FileExistsError: + raise FileExistsError(f"Output directory {out_dir} already exists") + scheme["primer_checksum"] = hash_bed(scheme_dir / "primer.bed") + scheme["reference_checksum"] = hash_ref(scheme_dir / "reference.fasta") + with open(out_dir / "info.yml", "w") as scheme_fh: + logger.debug(f"Writing info.yml to {out_dir}/info.yml") + yaml.dump(scheme, scheme_fh, sort_keys=False) + logger.debug(f"Copying primer.bed to {out_dir}/primer.bed") + with open(out_dir / "primer.bed", "w") as primer_fh: + primer_fh.write(format_primer_bed(scheme_dir / "primer.bed")) + logger.debug(f"Copying reference.fasta to {out_dir}/reference.fasta") + shutil.copy(scheme_dir / "reference.fasta", out_dir) + logger.debug(f"Writing scheme.bed to {out_dir}/scheme.bed") + scheme_bed_str = convert_primer_bed_to_scheme_bed( + bed_path=out_dir / "primer.bed" + ) + with open(out_dir.resolve() / "scheme.bed", "w") as fh: + fh.write(scheme_bed_str) + + if plot: + plot_primers( + bed_path=out_dir / "primer.bed", out_path=out_dir / "primer.svg" + ) + + logger.info(f"Built {scheme_cname}") + + +def get_scheme_cname(scheme: dict, sep: Literal["/", "_"] = "/") -> str: + organism = str(scheme.get("organism", "")) + name = str(scheme["name"]) + amplicon_size = str(scheme.get("amplicon_size", "")) + version = str(scheme["version"]) + return sep.join([organism, name, amplicon_size, version]) + + +def build_manifest(root_dir: Path, out_dir: Path = Path()): """Build manifest of schemes inside the specified directory""" - schema_path = get_primer_schemes_path() / "schema/manifest.json" - organisms = parse_yaml(Path(schema_dir) / "organisms.yml") - manifest = { - "schema_version": "0.9.0", - "metadata": "The PHA4GE list of tiling amplicon primer schemes", - "repository": "https://github.com/pha4ge/primer-schemes", - "latest_doi": "", - "license": "CC-BY-4.0", - "organisms": organisms, - } - - names_schemes = {} - families_names = defaultdict(list) - for entry in scan(root_dir): - if entry.is_file() and entry.name == "info.yml": - scheme = parse_yaml(entry.path) - name = scheme["name"] - names_schemes[name] = scheme - family, _, version = scheme["name"].partition("-") - families_names[family].append(name) - - families_data = [] - for family, names in sorted(families_names.items()): - family_data = {} - family_data["family"] = family - family_example_name = families_names[family][0] - family_data["organism"] = names_schemes[family_example_name]["organism"] - versions_data = [] - for name in sorted(names): - if names_schemes[name].get("display_name"): - display_name = names_schemes[name]["display_name"] - else: - display_name = name - versions_data.append( - { - "name": name, - "display_name": display_name, - "version": name.partition("-")[2], - "repository": names_schemes[name]["repository_url"], - } + + manifest = parse_yaml(MANIFEST_HEADER_PATH) + + manifest_field_exclude = [ + "schema_version", + ] + + scheme_path = root_dir / "schemes" + if not scheme_path.exists(): + scheme_path = root_dir + + schemes = [] + organism_set = set([o["organism"] for o in manifest["organisms"]]) + for scheme_info_path in scheme_path.glob("**/info.yml"): + scheme = parse_yaml(scheme_info_path) + for field in manifest_field_exclude: + if field in scheme: + del scheme[field] + if scheme["organism"] not in organism_set: + logger.warning( + f"Skipping scheme {scheme['name']} with unknown organism {scheme['organism']}", ) - logging.info(f"Reading {name}") - family_data["versions"] = versions_data - families_data.append(family_data) - manifest["schemes"] = families_data + schemes.append(scheme) + + manifest["schemes"] = sorted(schemes, key=get_scheme_cname) - manifest_file_name = "index.yml" + manifest_file_name = "index.json" with open(out_dir / manifest_file_name, "w") as fh: - logging.info(f"Writing {manifest_file_name} to {out_dir}/{manifest_file_name}") - yaml.dump(data=manifest, stream=fh, sort_keys=False) - validate_yaml_with_json_schema( - yaml_path=out_dir / manifest_file_name, schema_path=schema_path - ) + logger.info(f"Writing {manifest_file_name} to {out_dir}/{manifest_file_name}") + json.dump(manifest, fh, indent=4) def diff(bed1_path: Path, bed2_path: Path, only_positions: bool = False): @@ -407,28 +460,35 @@ def diff(bed1_path: Path, bed2_path: Path, only_positions: bool = False): return pd.concat([df1, df2]).drop_duplicates(subset=column_subset, keep=False) -def show_non_ref_alts(scheme_dir: Path): +def discordant_primers(scheme_dir: Path) -> pd.DataFrame: """Show primer records with sequences not matching the reference sequence""" - bed_path = scheme_dir / "primer.bed" - fasta_path = scheme_dir / "reference.fasta" + primer_bed_path = scheme_dir / "primer.bed" + scheme_bed_path = scheme_dir / "scheme.bed" with TemporaryDirectory() as temp_dir: - convert_scheme_bed_to_primer_bed( - bed_path=scheme_dir / "scheme.bed", - fasta_path=scheme_dir / "reference.fasta", - out_dir=temp_dir, - ) - return diff(bed1_path=bed_path, bed2_path=Path(temp_dir) / "primer.bed") - + backfilled_bed_path = Path(temp_dir) / "primer.bed" + if not scheme_bed_path.exists(): + with open(scheme_bed_path, "w") as fh: + fh.write(convert_primer_bed_to_scheme_bed(primer_bed_path)) + scheme_bed_path = Path(temp_dir) / "scheme.bed" + with open(backfilled_bed_path, "w") as fh: + fh.write( + convert_scheme_bed_to_primer_bed( + bed_path=scheme_dir / "scheme.bed", + fasta_path=scheme_dir / "reference.fasta", + ) + ) + return diff(bed1_path=primer_bed_path, bed2_path=backfilled_bed_path) -def compute_intervals(bed_path: Path) -> dict[str, dict[str, (int, int)]]: - # find primer positions for all primers in the bed file and compute maximum - # interval between primers of the same name - primer_name_re = re.compile(r'^(?P.*)_(LEFT|RIGHT)(_.+)?$') - eden_primer_name_re = re.compile(r'^(?P.*_[AB][0-9])(F|R)_\d+$') - all_intervals: dict[str, dict[str, (int, int)]] = {} +def amplicon_intervals(bed_path: Path) -> Dict[str, Dict[str, Tuple[int, int]]]: + """ + find primer positions for all primers in the bed file and compute maximum + interval between primers of the same name + """ + primer_name_re = re.compile(r"^(?P.*)_(LEFT|RIGHT)(_.+)?$") + all_intervals: dict[str, dict[str, Tuple[int, int]]] = {} for line in open(bed_path): - line_parts = line.strip().split('\t') + line_parts = line.strip().split("\t") if len(line_parts) < 6: # skip lines that don't have at least 6 fields continue @@ -438,17 +498,125 @@ def compute_intervals(bed_path: Path) -> dict[str, dict[str, (int, int)]]: intervals = all_intervals[chrom] primer_match = primer_name_re.match(name) if not primer_match: - # the Eden scheme has a unique primer name format - primer_match = eden_primer_name_re.match(name) - if not primer_name_re: - raise ValueError(f"Invalid primer name {name}") + raise ValueError(f"Invalid primer name {name}") primer_name = primer_match.group("name") - if strand == '+': + if strand == "+": start_pos = int(start) end_pos = -1 - if strand == '-': + if strand == "-": start_pos = sys.maxsize end_pos = int(end) prev_start, prev_end = intervals.get(primer_name, (sys.maxsize, -1)) intervals[primer_name] = (min(prev_start, start_pos), max(prev_end, end_pos)) return all_intervals + + +def plot_primers(bed_path: Path, out_path: Path = Path("primer.html")) -> None: + """ + Plot amplicon and primer positions from a 7 column primer.bed file + Requires primers to be named {$scheme_id}_{$amplicon_id}_{LEFT|RIGHT}_{1|2|3…} + Plots one vertical panel per pool per reference chromosome + Supported out_path extensions: html (interactive), pdf, png, svg + """ + primer_df = parse_primer_bed(bed_path) + primer_df["amplicon"] = primer_df["name"].str.split("_").str[1] + primer_df["poolName"] = primer_df["poolName"].astype(str) + + amp_df = ( + primer_df.groupby(["chrom", "amplicon", "poolName"]) + .agg(min_start=("chromStart", "min"), max_end=("chromEnd", "max")) + .reset_index() + ) + amp_df["is_amplicon"] = True + primer_df["is_amplicon"] = False + amp_df = amp_df.rename(columns={"min_start": "chromStart", "max_end": "chromEnd"}) + combined_df = pd.concat([primer_df, amp_df], ignore_index=True) + + primer_marks = ( + alt.Chart(combined_df) + .transform_filter(alt.datum.is_amplicon == False) # noqa + .mark_line(size=15) + .encode( + x=alt.X("chromStart:Q", title=None), + x2="chromEnd:Q", + y=alt.Y("poolName:O", title="pool", scale=alt.Scale(padding=1)), + color=alt.Color("strand:N").scale(scheme="set2"), + tooltip=[ + alt.Tooltip("name:N", title="Primer name"), + alt.Tooltip("chromStart:Q", title="start"), + alt.Tooltip("chromEnd:Q", title="end"), + ], + ) + .properties( + width=800, + ) + ) + amplicon_marks = ( + alt.Chart(combined_df) + .transform_filter(alt.datum.is_amplicon == True) # noqa + .mark_rule(strokeWidth=2) + .encode( + x=alt.X("chromStart:Q", title=None), + x2="chromEnd:Q", + y=alt.Y("poolName:O", title="pool", scale=alt.Scale(padding=1)), + tooltip=[ + alt.Tooltip("amplicon:N", title="Amplicon name"), + alt.Tooltip("chromStart:Q", title="Min primer start"), + alt.Tooltip("chromEnd:Q", title="Max primer end"), + ], + ) + .properties( + width=800, + ) + ) + combined_chart = ( + alt.layer(primer_marks, amplicon_marks) + .facet(row=alt.Row("chrom:O", header=alt.Header(labelOrient="top"), title="")) + .configure_axis(domain=False, ticks=False) + ) + + combined_chart.interactive().save(str(out_path)) + logger.info(f"Plot saved ({out_path})") + + +def subset(scheme_dir: Path, chrom: str, out_dir: Path = Path("built")) -> None: + scheme_dir = Path(scheme_dir) + out_dir.mkdir(parents=True, exist_ok=True) + reference_chroms = set() + subset_record = None + for record in SeqIO.parse(scheme_dir / "reference.fasta", "fasta"): + reference_chroms.add(record.id) + if record.id == chrom: + subset_record = record + if not subset_record: + raise ValueError(f"Chrom {chrom} not found in reference.fasta") + else: + with open(out_dir / "reference.fasta", "w") as fh: + SeqIO.write(subset_record, fh, "fasta") + + primers_df = parse_primer_bed(scheme_dir / "primer.bed") + primers_df["chrom"] = primers_df["chrom"].str.partition(" ")[0] + primer_chroms = set(primers_df["chrom"].unique()) + subset_primers_df = primers_df.query(f"chrom == '{chrom}'") + subset_primers_df.to_csv( + out_dir / "primer.bed", sep="\t", index=False, header=False + ) + + if reference_chroms != primer_chroms: + logger.info(f"Reference chroms: {reference_chroms}") + logger.info(f"Primer chroms: {primer_chroms}") + else: + logger.info(f"Chroms: {reference_chroms}") + + logger.info( + f"Wrote subset of {len(subset_primers_df)}/{len(primers_df)} primers for {chrom} to {out_dir.resolve()}" + ) + + +def synchronise() -> None: + util.download_github_tarball(SCHEMES_ARCHIVE_URL, CACHE_DIR) + + +# def fetch(string: str) -> None: +# with open(CACHE_DIR / "index.json", "r") as fh: +# manifest = json.load(fh) diff --git a/src/primaschema/schema/__init__.py b/src/primaschema/schema/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/src/primaschema/schema/bed.py b/src/primaschema/schema/bed.py new file mode 100644 index 0000000..aee3782 --- /dev/null +++ b/src/primaschema/schema/bed.py @@ -0,0 +1,150 @@ +from pydantic import ( + BaseModel, + ConfigDict, + NonNegativeInt, + computed_field, + model_validator, +) +from typing import Dict, List, Literal, Optional, Tuple + + +class PrimerModel(BaseModel): + """A primer as represented by a BED record in Primal Scheme v3 format""" + + model_config = ConfigDict(str_strip_whitespace=True) + chrom: str + chrom_start: NonNegativeInt + chrom_end: NonNegativeInt + name: str + pool_name: int + strand: Literal["+", "-"] + sequence: str + + @computed_field + @property + def name_parts(self) -> List[str]: + parts = self.name.split("_") + if len(parts) != 4: + raise ValueError( + "Name must be in the format '{name}_{amplicon-number}_{LEFT|RIGHT}_{primer-number}'" + ) + return parts + + @computed_field + @property + def number(self) -> int: + return int(self.name.split("_")[3]) + + +class AmpliconModel(BaseModel): + """An amplicon as represented by two or more primer records""" + + primers: List[PrimerModel] + + @computed_field + @property + def number(self) -> int: + return int(self.primers[0].name_parts[1]) + + @computed_field + @property + def min_start(self) -> int: + return min(p.chrom_start for p in self.primers) + + @computed_field + @property + def max_end(self) -> int: + return max(p.chrom_end for p in self.primers) + + +class BedModel(BaseModel): + """A BED file as represented by a collection of amplicons each comprising primer records""" + + amplicons: Dict[str, List[AmpliconModel]] + reference_lengths: Optional[Dict[str, int]] = None + + @model_validator(mode="after") + def check_duplicate_primer_names(self) -> "BedModel": + primer_names = [] + for chrom, amplicons in self.amplicons.items(): + for amplicon in amplicons: + for primer in amplicon.primers: + primer_names.append(primer.name) + if not len(primer_names) == len(set(primer_names)): + raise ValueError("Duplicate primer names detected") + return self + + @model_validator(mode="after") + def check_primer_bounds(self) -> "BedModel": + if self.reference_lengths: + ref_lens = self.reference_lengths + for chrom, amplicons in self.amplicons.items(): + for amplicon in amplicons: + if chrom not in ref_lens: + raise ValueError( + f"Reference chromosome {chrom} not found in reference.fasta" + ) + if not amplicon.max_end <= ref_lens[chrom]: + raise ValueError( + f"A primer in amplicon {amplicon.number} is beyond the bounds of {chrom}" + ) + return self + + @model_validator(mode="after") + def check_primer_tiling(self) -> "BedModel": + chroms_amplicon_boundaries = {} + for chrom, amplicons in self.amplicons.items(): + chrom = chrom.partition(" ")[0] + chroms_amplicon_boundaries[chrom] = [ + (a.min_start, a.max_end) for a in amplicons + ] + for chrom, amplicon_boundaries in chroms_amplicon_boundaries.items(): + BedModel.check_tiling(amplicon_boundaries) + return self + + @staticmethod + def check_overlap(interval1: Tuple[int, int], interval2: Tuple[int, int]) -> bool: + """Check if two intervals overlap""" + return max(interval1[0], interval2[0]) <= min(interval1[1], interval2[1]) + + @staticmethod + def check_tiling(intervals: List[Tuple[int, int]]): + """Verify if each interval overlaps exactly once with the interval before it and after it, + and does not overlap with any other interval""" + n = len(intervals) + if n < 2: + raise ValueError("Fewer than two amplicons detected") + + # Check first interval + if not BedModel.check_overlap(intervals[0], intervals[1]): + raise ValueError("First and second amplicons do not overlap") + for j in range(2, n): + if BedModel.check_overlap(intervals[0], intervals[j]): + raise ValueError( + f"First amplicon overlaps with more than one amplicon ({j})" + ) + + # Check last interval + if not BedModel.check_overlap(intervals[-1], intervals[-2]): + raise ValueError("Penultimate and last amplicons do not overlap") + for j in range(n - 2): + if BedModel.check_overlap(intervals[-1], intervals[j]): + raise ValueError( + f"Last amplicon overlaps with more than one amplicon ({j})" + ) + + # Check other intervals + for i in range(1, n - 1): + if not ( + BedModel.check_overlap(intervals[i], intervals[i - 1]) + and BedModel.check_overlap(intervals[i], intervals[i + 1]) + ): + raise ValueError(f"Amplicons {i-1} and {i} do not overlap") + + # Check interval overlaps only with previous and next + for j in range(n): + if j != i - 1 and j != i + 1 and j != i: + if BedModel.check_overlap(intervals[i], intervals[j]): + raise ValueError( + f"Amplicon {i} overlaps with more than two other amplicons ({j})" + ) diff --git a/src/primaschema/schema/info.py b/src/primaschema/schema/info.py new file mode 100644 index 0000000..be30875 --- /dev/null +++ b/src/primaschema/schema/info.py @@ -0,0 +1,164 @@ +from __future__ import annotations +from enum import Enum +import re +from typing import List, Optional +from pydantic.version import VERSION as PYDANTIC_VERSION + +if int(PYDANTIC_VERSION[0]) >= 2: + from pydantic import BaseModel, ConfigDict, Field, field_validator +else: + from pydantic import BaseModel, Field + +metamodel_version = "None" +version = "1.0.0-alpha" + + +class ConfiguredBaseModel(BaseModel): + model_config = ConfigDict( + validate_assignment=True, + validate_default=True, + extra="forbid", + arbitrary_types_allowed=True, + use_enum_values=True, + strict=False, + ) + pass + + +class SchemeStatus(str, Enum): + """ + Status of this amplicon primer scheme + """ + + PUBLISHED = "PUBLISHED" + DEPRECATED = "DEPRECATED" + DRAFT = "DRAFT" + + +class PrimerScheme(ConfiguredBaseModel): + """ + A tiled amplicon PCR primer scheme definition + """ + + schema_version: str = Field( + ..., + description="""The version of the schema used to create this scheme definition""", + ) + name: str = Field( + ..., description="""The canonical name of the primer scheme (lowercase)""" + ) + amplicon_size: int = Field( + ..., + description="""The length (in base pairs) of an amplicon in the primer scheme""", + ge=1, + ) + version: str = Field(...) + organism: str = Field( + ..., + description="""The organism against which this primer scheme is targeted. Lowercase, e.g. sars-cov-2""", + ) + source_url: Optional[str] = Field( + None, + description="""Source URL of primer scheme BED file, if available, e.g. GitHub repository URL""", + ) + definition_url: Optional[str] = Field( + None, + description="""GitHub URL of PHA4GE compatible primer scheme scheme definition""", + ) + aliases: Optional[List[str]] = Field( + default_factory=list, description="""Aliases for primer scheme name""" + ) + license: Optional[str] = Field( + None, description="""License under which the primer scheme is distributed""" + ) + status: Optional[SchemeStatus] = Field( + "PUBLISHED", + description="""The status of this primer scheme (e.g. published, deprecated)""", + ) + derived_from: Optional[str] = Field( + None, + description="""Canonical name of the primer scheme from which this scheme was derived""", + ) + developers: List[str] = Field( + default_factory=list, + description="""Persons or organisations responsible for developing the primer scheme""", + ) + citations: Optional[List[str]] = Field( + default_factory=list, + description="""URLs of publications describing the scheme (DOIs preferred when available)""", + ) + notes: Optional[List[str]] = Field( + default_factory=list, description="""Notes about the amplicon primer scheme""" + ) + vendors: Optional[List[Vendor]] = Field( + default_factory=list, + description="""Vendors where one can purchase the primers described in the amplicon scheme or a kit containing these primers""", + ) + masks: Optional[List[Mask]] = Field( + default_factory=list, + description="""Regions of the reference genome that should be masked out with N""", + ) + primer_checksum: Optional[str] = Field( + None, + description="""Checksum for the primer scheme BED file, in format checksum_type:checksum, where checksum_type is lowercase name of checksum generator e.g. primaschema""", + ) + reference_checksum: Optional[str] = Field( + None, + description="""Checksum for the reference FASTA file, in format checksum_type:checksum, where checksum_type is lowercase name of checksum generator e.g. primaschema""", + ) + + @field_validator("name") + def pattern_name(cls, v): + pattern = re.compile(r"^[\da-z0-9_.-]+$") + if isinstance(v, list): + for element in v: + if not pattern.match(element): + raise ValueError(f"Invalid name format: {element}") + elif isinstance(v, str): + if not pattern.match(v): + raise ValueError(f"Invalid name format: {v}") + return v + + @field_validator("version") + def pattern_version(cls, v): + pattern = re.compile(r"^[\da-z0-9_.-]+$") + if isinstance(v, list): + for element in v: + if not pattern.match(element): + raise ValueError(f"Invalid version format: {element}") + elif isinstance(v, str): + if not pattern.match(v): + raise ValueError(f"Invalid version format: {v}") + return v + + +class Vendor(ConfiguredBaseModel): + """ + Vendor of the primers described in the amplicon scheme or a kit containing these primers + """ + + organisation_name: str = Field(..., description="""The name of the vendor""") + home_page: Optional[str] = Field( + None, description="""A link to the home page of the vendor""" + ) + kit_name: Optional[str] = Field( + None, description="""Vendor specific kit name for primer kit""" + ) + + +class Mask(ConfiguredBaseModel): + """ + A region to mask out, with zero-based, half open coordinates + """ + + reference: str = Field(..., description="""Name (ID) of the reference sequence""") + name: str = Field(..., description="""Name of the region""") + start: int = Field(..., description="""Start coordinate of the region""", ge=1) + end: int = Field(..., description="""End coordination of the region""", ge=1) + + +# Model rebuild +# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model +PrimerScheme.model_rebuild() +Vendor.model_rebuild() +Mask.model_rebuild() diff --git a/src/primaschema/schema/info.yml b/src/primaschema/schema/info.yml new file mode 100644 index 0000000..cd3c97a --- /dev/null +++ b/src/primaschema/schema/info.yml @@ -0,0 +1,168 @@ +id: https://github.com/pha4ge/primer-schemes/schemas/primer-scheme +name: primer-scheme +description: Data model for tiling primer scheme definitions +version: 1.0.0-alpha +prefixes: + linkml: https://w3id.org/linkml/ + schema: http://schema.org/ + ORCID: http://identifiers.org/orcid/ + GENEPIO: http://purl.obolibrary.org/obo/GENEPIO_ + IAO: "https://bioregistry.io/reference/iao:" +default_curi_maps: + - semweb_context +imports: + - linkml:types +default_range: string + +classes: + PrimerScheme: + tree_root: true + description: "A tiled amplicon PCR primer scheme definition" + slots: + - schema_version + - name + - amplicon_size + - version + - organism + - source_url + - definition_url + - aliases + - license + - status + - derived_from + - developers + - citations + - notes + - vendors + - masks + - primer_checksum + - reference_checksum + + Vendor: + class_uri: GENEPIO:0100674 + description: "Vendor of the primers described in the amplicon scheme or a kit containing these primers" + attributes: + organisation_name: + description: "The name of the vendor" + required: true + home_page: + description: "A link to the home page of the vendor" + kit_name: + slot_uri: GENEPIO:0100693 + description: "Vendor specific kit name for primer kit" + + Mask: + description: "A region to mask out, with zero-based, half open coordinates" + attributes: + reference: + description: "Name (ID) of the reference sequence" + required: true + name: + description: "Name of the region" + required: true + start: + description: "Start coordinate of the region" + range: integer + minimum_value: 1 + required: true + end: + description: "End coordination of the region" + range: integer + minimum_value: 1 + required: true + +slots: + schema_version: + required: true + description: The version of the schema used to create this scheme definition + name: + slot_uri: GENEPIO:0001456 + required: true + identifier: true + description: The canonical name of the primer scheme (lowercase) + pattern: "^[\\da-z0-9_.-]+$" + version: + required: true + pattern: "^[\\da-z0-9_.-]+$" + display_name: + description: The human-friendly display name of the primer scheme + organism: + slot_uri: GENEPIO:0100682 + required: true + description: The organism against which this primer scheme is targeted. Lowercase, e.g. sars-cov-2 + aliases: + slot_uri: GENEPIO:0100670 + description: Aliases for primer scheme name + multivalued: true + inlined_as_list: true + developers: + slot_uri: GENEPIO:0100673 + description: Persons or organisations responsible for developing the primer scheme + required: true + multivalued: true + vendors: + description: "Vendors where one can purchase the primers described in the amplicon scheme or a kit containing these primers" + multivalued: true + inlined_as_list: true + range: Vendor + amplicon_size: + slot_uri: GENEPIO:0001449 + description: "The length (in base pairs) of an amplicon in the primer scheme" + range: integer + required: true + minimum_value: 1 + definition_url: + slot_uri: GENEPIO:0100683 + description: "GitHub URL of PHA4GE compatible primer scheme scheme definition" + source_url: + description: "Source URL of primer scheme BED file, if available, e.g. GitHub repository URL" + notes: + description: "Notes about the amplicon primer scheme" + slot_uri: GENEPIO:0100672 + multivalued: true + inlined_as_list: true + range: string + status: + slot_uri: GENEPIO:0100681 + description: "The status of this primer scheme (e.g. published, deprecated)" + range: SchemeStatus + ifabsent: string(PUBLISHED) + license: + description: "License under which the primer scheme is distributed" + citations: + slot_uri: IAO:0000301 + description: "URLs of publications describing the scheme (DOIs preferred when available)" + multivalued: true + inlined_as_list: true + primer_checksum: + slot_uri: GENEPIO:0100675 + description: "Checksum for the primer scheme BED file, in format checksum_type:checksum, where checksum_type is lowercase name of checksum generator e.g. primaschema" + reference_checksum: + description: "Checksum for the reference FASTA file, in format checksum_type:checksum, where checksum_type is lowercase name of checksum generator e.g. primaschema" + derived_from: + slot_uri: GENEPIO:0100671 + description: "Canonical name of the primer scheme from which this scheme was derived" + person_name: + slot_uri: schema:name + required: true + description: "The name of a natural person" + orcid: + description: "ORCID ('Open Researcher and Contributor IDentifier') of a person" + organisation_name: + required: true + description: "The name of an organisation" + home_page: + description: "A link to the home page of an organisation" + masks: + description: "Regions of the reference genome that should be masked out with N" + multivalued: true + inlined_as_list: true + range: Mask + +enums: + SchemeStatus: + description: "Status of this amplicon primer scheme" + permissible_values: + PUBLISHED: + DEPRECATED: + DRAFT: diff --git a/src/primaschema/schema/manifest-header.yml b/src/primaschema/schema/manifest-header.yml new file mode 100644 index 0000000..3065e59 --- /dev/null +++ b/src/primaschema/schema/manifest-header.yml @@ -0,0 +1,17 @@ +schema_version: "1.0.0-alpha" +metadata: The manifest of PHA4GE tiled amplicon PCR primer scheme definitions +repository: https://github.com/pha4ge/primer-schemes +license: CC-BY-4.0 +organisms: +- organism: sars-cov-2 + display_name: SARS-CoV-2 + aliases: + - nCoV-2019 +- organism: mpxv + display_name: MPXV + aliases: + - Monkeypox virus +- organism: niv + display_name: NiV + aliases: + - Nipah virus diff --git a/src/primaschema/util.py b/src/primaschema/util.py new file mode 100644 index 0000000..413959e --- /dev/null +++ b/src/primaschema/util.py @@ -0,0 +1,56 @@ +import subprocess +import shutil +import tarfile + +from io import BytesIO +from pathlib import Path + +import httpx + +from . import logger + + +def run(cmd, cwd="./"): # Helper for CLI testing + return subprocess.run( + cmd, cwd=cwd, shell=True, check=True, text=True, capture_output=True + ) + + +def copy_single_child_dir_to_parent(parent_dir_path: Path) -> None: + parent_dir = Path(parent_dir_path) + child_dirs = [ + d for d in parent_dir.iterdir() if d.is_dir() and not d.name.startswith(".") + ] + if len(child_dirs) != 1: + raise FileNotFoundError( + f"Expected one child directory not starting with a dot, but found {len(child_dirs)}." + ) + child_dir = child_dirs[0] + + for item in child_dir.iterdir(): + destination = parent_dir / item.name + if item.is_dir(): + shutil.copytree(item, destination, dirs_exist_ok=True) + else: + shutil.copy2(item, destination) + + shutil.rmtree(child_dir) + + +def download_github_tarball(archive_url: str, out_dir: Path) -> None: + if not archive_url.endswith(".tar.gz"): + raise ValueError("Archive URL must end with .tar.gz") + + out_dir = Path(out_dir) + out_dir.mkdir(parents=True, exist_ok=True) + + response = httpx.get(archive_url, follow_redirects=True) + response.raise_for_status() + + shutil.rmtree(out_dir, ignore_errors=True) + with tarfile.open(fileobj=BytesIO(response.content), mode="r:gz") as tf_fh: + tf_fh.extractall(out_dir) + + copy_single_child_dir_to_parent(out_dir) + + logger.info(f"Schemes downloaded and extracted to {out_dir}") diff --git a/test/data/bed-comment/info.yml b/test/data/bed-comment/info.yml new file mode 100644 index 0000000..f7b23f4 --- /dev/null +++ b/test/data/bed-comment/info.yml @@ -0,0 +1,22 @@ +schema_version: 1.0.0a +organism: sars-cov-2 +name: artic +amplicon_size: 400 +version: v4.1.0 +derived_from: sars-cov-2/artic/400/v4.0.0 +aliases: +- ARTIC/V4.1 +developers: +- ARTIC network +vendors: +- organisation_name: IDT + kit_name: '10011442' +- organisation_name: Eurofins + home_page: https://eurofinsgenomics.com +definition_url: https://github.com/pha4ge/primer-schemes/tree/main/sars-cov-2/artic/v4.1 +source_url: https://github.com/quick-lab/primerschemes/tree/main/primerschemes/artic-sars-cov-2/400/v4.1.0 +citations: +- https://doi.org/10.1101%2F2020.09.04.283077 +license: CC-BY-SA-4.0 +primer_checksum: primaschema:3ef3e7bb23008684 +reference_checksum: primaschema:b1acd7163146bf17 diff --git a/test/data/bed-comment/primer.bed b/test/data/bed-comment/primer.bed new file mode 100644 index 0000000..7c37459 --- /dev/null +++ b/test/data/bed-comment/primer.bed @@ -0,0 +1,210 @@ +# Ignored line +MN908947.3 25 50 SARS-CoV-2_1_LEFT_1 1 + AACAAACCAACCAACTTTCGATCTC +MN908947.3 408 431 SARS-CoV-2_1_RIGHT_1 1 - CTTCTACTAAGCCACAAGTGCCA +MN908947.3 324 344 SARS-CoV-2_2_LEFT_1 2 + TTTACAGGTTCGCGACGTGC +MN908947.3 705 727 SARS-CoV-2_2_RIGHT_1 2 - ATAAGGATCAGTGCCAAGCTCG +MN908947.3 644 666 SARS-CoV-2_3_LEFT_1 1 + GTAATAAAGGAGCTGGTGGCCA +MN908947.3 1017 1044 SARS-CoV-2_3_RIGHT_1 1 - GCCAATTTAATTTCAAAAGGTGTCTGC +MN908947.3 944 966 SARS-CoV-2_4_LEFT_1 2 + GTGTATACTGCTGCCGTGAACA +MN908947.3 1337 1362 SARS-CoV-2_4_RIGHT_1 2 - ACAACAGCATTTTGGGGTAAGTAAC +MN908947.3 1245 1266 SARS-CoV-2_5_LEFT_1 1 + TGAAACTTCATGGCAGACGGG +MN908947.3 1623 1650 SARS-CoV-2_5_RIGHT_1 1 - TTGATGTTGACTTTCTCTTTTTGGAGT +MN908947.3 1540 1562 SARS-CoV-2_6_LEFT_1 2 + CGTGCTAGCGCTAACATAGGTT +MN908947.3 1925 1948 SARS-CoV-2_6_RIGHT_1 2 - AACACGCACAGAATTTTGAGCAG +MN908947.3 1851 1875 SARS-CoV-2_7_LEFT_1 1 + ACTGAGTCCTCTTTATGCATTTGC +MN908947.3 2228 2250 SARS-CoV-2_7_RIGHT_1 1 - CCACCGACAATTTCACAAGCAC +MN908947.3 2154 2180 SARS-CoV-2_8_LEFT_1 2 + GCTTGAAGAGAAGTTTAAGGAAGGTG +MN908947.3 2544 2571 SARS-CoV-2_8_RIGHT_1 2 - GGTTGTTCTAATGGTTGTAAATCACCA +MN908947.3 2483 2508 SARS-CoV-2_9_LEFT_1 1 + TCTTCTTAGAGGGAGAAACACTTCC +MN908947.3 2861 2885 SARS-CoV-2_9_RIGHT_1 1 - CACAGGCGAACTCATTTACTTCTG +MN908947.3 2780 2813 SARS-CoV-2_10_LEFT_1 2 + TGAATATCACTTTTGAACTTGATGAAAGGATTG +MN908947.3 2826 2850 SARS-CoV-2_10_LEFT_2 2 + TGAGAAGTGCTCTGCCTATACAGT +MN908947.3 3156 3177 SARS-CoV-2_10_RIGHT_1 2 - GGTTGAAGAGCAGCAGAAGTG +MN908947.3 3183 3210 SARS-CoV-2_10_RIGHT_2 2 - TCATCTAACCAATCTTCTTCTTGCTCT +MN908947.3 3078 3102 SARS-CoV-2_11_LEFT_1 1 + AGAAGAGTTTGAGCCATCAACTCA +MN908947.3 3470 3492 SARS-CoV-2_11_RIGHT_1 1 - TTTAAGGCTCCTGCAACACCTC +MN908947.3 3390 3412 SARS-CoV-2_12_LEFT_1 2 + TGCAGACATTGTGGAAGAAGCT +MN908947.3 3769 3794 SARS-CoV-2_12_RIGHT_1 2 - CAGCTAAGTAGACATTTGTGCGAAC +MN908947.3 3683 3705 SARS-CoV-2_13_LEFT_1 1 + AGCACGAAGTTCTACTTGCACC +MN908947.3 4067 4093 SARS-CoV-2_13_RIGHT_1 1 - GATGTCAATGTCACTAACAAGAGTGG +MN908947.3 3992 4018 SARS-CoV-2_14_LEFT_1 2 + TGGAAGAAACTAAGTTCCTCACAGAA +MN908947.3 4387 4409 SARS-CoV-2_14_RIGHT_1 2 - CATGTGCAAGCATTTCTCGCAA +MN908947.3 4312 4339 SARS-CoV-2_15_LEFT_1 1 + AAAAGTGCCTTTTACATTCTACCATCT +MN908947.3 4685 4710 SARS-CoV-2_15_RIGHT_1 1 - GCATCAGGTGAAGAAACAGAAACTG +MN908947.3 4620 4648 SARS-CoV-2_16_LEFT_1 2 + TGTAACACATGGCTTAAATTTGGAAGAA +MN908947.3 4995 5017 SARS-CoV-2_16_RIGHT_1 2 - CACAACTTGCGTGTGGAGGTTA +MN908947.3 4923 4953 SARS-CoV-2_17_LEFT_1 1 + TGACAATCTTAAGACACTTCTTTCTTTGAG +MN908947.3 5302 5331 SARS-CoV-2_17_RIGHT_1 1 - TTCAACTCTATTTGTTGGAGTGTTAACAA +MN908947.3 5230 5259 SARS-CoV-2_18_LEFT_1 2 + TGGAAATACCCACAAGTTAATGGTTTAAC +MN908947.3 5620 5643 SARS-CoV-2_18_RIGHT_1 2 - GCTTGTTTACCACACGTACAAGG +MN908947.3 5561 5584 SARS-CoV-2_19_LEFT_1 1 + AAGCTGTTATGTACATGGGCACA +MN908947.3 5932 5957 SARS-CoV-2_19_RIGHT_1 1 - TGTCCAACTTAGGGTCAATTTCTGT +MN908947.3 5867 5894 SARS-CoV-2_20_LEFT_1 2 + ACAAAGAAAACAGTTACACAACAACCA +MN908947.3 6247 6272 SARS-CoV-2_20_RIGHT_1 2 - ACGTGGCTTTATTAGTTGCATTGTT +MN908947.3 6184 6210 SARS-CoV-2_21_LEFT_1 1 + CACTACACACCCTCTTTTAAGAAAGG +MN908947.3 6553 6582 SARS-CoV-2_21_RIGHT_1 1 - GTAAGACTAGAATTGTCTACATAAGCAGC +MN908947.3 6478 6507 SARS-CoV-2_22_LEFT_1 2 + GTAGGAGACATTATACTTAAACCAGCAAA +MN908947.3 6859 6885 SARS-CoV-2_22_RIGHT_1 2 - CCGACACTCTTAACAGTATTCTTTGC +MN908947.3 6747 6776 SARS-CoV-2_23_LEFT_1 1 + AAACCGTGTTTGTACTAATTATATGCCTT +MN908947.3 7122 7148 SARS-CoV-2_23_RIGHT_1 1 - AACCACTAAGACAAACACTACAAGGT +MN908947.3 7127 7156 SARS-CoV-2_23_RIGHT_2 1 - AGAATCTAAACCACTAAGACAAACACTAC +MN908947.3 7057 7084 SARS-CoV-2_24_LEFT_1 2 + GGTTACAGAGAAGGCTATTTGAACTCT +MN908947.3 7440 7467 SARS-CoV-2_24_RIGHT_1 2 - ACAACATGCACATAACTTTTCCATACA +MN908947.3 7381 7403 SARS-CoV-2_25_LEFT_1 1 + CAAATGGCCCCGATTTCAGCTA +MN908947.3 7747 7770 SARS-CoV-2_25_RIGHT_1 1 - TGGATGGAACCATTCTTCACTGT +MN908947.3 7672 7695 SARS-CoV-2_26_LEFT_1 2 + GCGAGAGACTTGTCACTACAGTT +MN908947.3 8063 8092 SARS-CoV-2_26_RIGHT_1 2 - GAGTTTTTCCATTGGTACGTTAAAAGTTG +MN908947.3 7997 8019 SARS-CoV-2_27_LEFT_1 1 + CTGATGTTGGTGATAGTGCGGA +MN908947.3 8367 8392 SARS-CoV-2_27_RIGHT_1 1 - AATGTTGTGACTTTTTGCTACCTGC +MN908947.3 8370 8395 SARS-CoV-2_27_RIGHT_2 1 - AGCAATGTTGTGACTTTTTGCTACC +MN908947.3 8304 8326 SARS-CoV-2_28_LEFT_1 2 + TGAAAACATGACACCCCGTGAC +MN908947.3 8691 8714 SARS-CoV-2_28_RIGHT_1 2 - TGACACCACCATCAATAGCCTTG +MN908947.3 8596 8619 SARS-CoV-2_29_LEFT_1 1 + CTTGTGTTCCTTTTTGTTGCTGC +MN908947.3 8990 9013 SARS-CoV-2_29_RIGHT_1 1 - AGCCAAAACACAAGCTGATGTTG +MN908947.3 8919 8944 SARS-CoV-2_30_LEFT_1 2 + ACCTAGAGTTTTTAGTGCAGTTGGT +MN908947.3 9306 9329 SARS-CoV-2_30_RIGHT_1 2 - CTACACCACAGAAAACTCCTGGT +MN908947.3 9168 9192 SARS-CoV-2_31_LEFT_1 1 + CCTTGAAGGTTCTGTTAGAGTGGT +MN908947.3 9535 9564 SARS-CoV-2_31_RIGHT_1 1 - AATGAGTAAACTGGTGTTAAACAGAGTAC +MN908947.3 9470 9497 SARS-CoV-2_32_LEFT_1 2 + GAGCTTTTGGTGAATACAGTCATGTAG +MN908947.3 9842 9866 SARS-CoV-2_32_RIGHT_1 2 - GAGGTAATAGCACATCACTACGCA +MN908947.3 9782 9805 SARS-CoV-2_33_LEFT_1 1 + GTACTTTTGAAGAAGCTGCGCTG +MN908947.3 10150 10176 SARS-CoV-2_33_RIGHT_1 1 - TGTCTTGGACAGTAAACTACGTCATC +MN908947.3 10076 10099 SARS-CoV-2_34_LEFT_1 2 + TCCCATCTGGTAAAGTTGAGGGT +MN908947.3 10465 10491 SARS-CoV-2_34_RIGHT_1 2 - CCACATGAACCATTAAGGAATGAACC +MN908947.3 10393 10419 SARS-CoV-2_35_LEFT_1 1 + GTGTTAGCTTGTTACAATGGTTCACC +MN908947.3 10785 10810 SARS-CoV-2_35_RIGHT_1 1 - AGGTCCTAGTATGTCAACATGGTCT +MN908947.3 10713 10742 SARS-CoV-2_36_LEFT_1 2 + CAATCGATTTACCACAACTCTTAATGACT +MN908947.3 11092 11116 SARS-CoV-2_36_RIGHT_1 2 - ACCCATAGCAAAAGGTAAAAAGGC +MN908947.3 11000 11023 SARS-CoV-2_37_LEFT_1 1 + CACACCACTGGTTGTTACTCACA +MN908947.3 11388 11414 SARS-CoV-2_37_RIGHT_1 1 - GTGTCAAGACATTCATAAGTGTCCAC +MN908947.3 11305 11330 SARS-CoV-2_38_LEFT_1 2 + GACTGTGTTATGTATGCATCAGCTG +MN908947.3 11689 11720 SARS-CoV-2_38_RIGHT_1 2 - CCTGTGTAGAAACTAAGTAATCATAAACACC +MN908947.3 11624 11651 SARS-CoV-2_39_LEFT_1 1 + GCTATTTTTGTACTTGTTACTTTGGCC +MN908947.3 12011 12033 SARS-CoV-2_39_RIGHT_1 1 - CCCTGCATGGAAAGCAAAACAG +MN908947.3 11937 11963 SARS-CoV-2_40_LEFT_1 2 + TGTCCAGTTACACAATGACATTCTCT +MN908947.3 12317 12339 SARS-CoV-2_40_RIGHT_1 2 - ACTTTTGCCCTCTTGTCCTCAG +MN908947.3 12234 12255 SARS-CoV-2_41_LEFT_1 1 + ATTTGACCGTGATGCAGCCAT +MN908947.3 12618 12643 SARS-CoV-2_41_RIGHT_1 1 - AAGAGGCCATGCTAAATTAGGTGAA +MN908947.3 12519 12546 SARS-CoV-2_42_LEFT_1 2 + TGGTACAACATTTACTTATGCATCAGC +MN908947.3 12895 12920 SARS-CoV-2_42_RIGHT_1 2 - TGTCTGTAACAAACCTACAAGGTGG +MN908947.3 12831 12856 SARS-CoV-2_43_LEFT_1 1 + GGATTTGAAATGGGCTAGATTCCCT +MN908947.3 13218 13240 SARS-CoV-2_43_RIGHT_1 1 - CGATGCACCACCAAAGGATTCT +MN908947.3 13124 13148 SARS-CoV-2_44_LEFT_1 2 + GGGGACAACCAATCACTAATTGTG +MN908947.3 13506 13528 SARS-CoV-2_44_RIGHT_1 2 - CATCAGTACTAGTGCCTGTGCC +MN908947.3 13463 13485 SARS-CoV-2_45_LEFT_1 1 + TAAACGGGTTTGCGGTGTAAGT +MN908947.3 13833 13859 SARS-CoV-2_45_RIGHT_1 1 - TCACAATTACCTTCATCAAAATGCCT +MN908947.3 13752 13775 SARS-CoV-2_46_LEFT_1 2 + AGAATAGACGGTGACATGGTACC +MN908947.3 14120 14144 SARS-CoV-2_46_RIGHT_1 2 - TCTACAACAGGAACTCCACTACCT +MN908947.3 14045 14075 SARS-CoV-2_47_LEFT_1 1 + TGGTGTACTGACATTAGATAATCAAGATCT +MN908947.3 14428 14457 SARS-CoV-2_47_RIGHT_1 1 - TGGAACACCATCAACAAATATTTTTCTCA +MN908947.3 14338 14362 SARS-CoV-2_48_LEFT_1 2 + ACTGTTTGGATGACAGATGCATTC +MN908947.3 14717 14743 SARS-CoV-2_48_RIGHT_1 2 - CAGAACTTCCTTCCTTAAAGAAACCC +MN908947.3 14647 14674 SARS-CoV-2_49_LEFT_1 1 + ACAATGTTGCTTTTCAAACTGTCAAAC +MN908947.3 15023 15050 SARS-CoV-2_49_RIGHT_1 1 - GGGATGACATTACGTTTTGTATATGCG +MN908947.3 14953 14983 SARS-CoV-2_50_LEFT_1 2 + CATTTAATAAATGGGGTAAGGCTAGACTTT +MN908947.3 15336 15358 SARS-CoV-2_50_RIGHT_1 2 - GAGCAAGAACAAGTGAGGCCAT +MN908947.3 15214 15237 SARS-CoV-2_51_LEFT_1 1 + GCAAATTCTATGGTGGTTGGCAC +MN908947.3 15596 15619 SARS-CoV-2_51_RIGHT_1 1 - GTCTGTGTTGTAAATTGCGGACA +MN908947.3 15535 15557 SARS-CoV-2_52_LEFT_1 2 + CTGTCACGGCCAATGTTAATGC +MN908947.3 15917 15941 SARS-CoV-2_52_RIGHT_1 2 - GGATCTGGGTAAGGAAGGTACACA +MN908947.3 15855 15881 SARS-CoV-2_53_LEFT_1 1 + ACTAAAGGACCTCATGAATTTTGCTC +MN908947.3 16239 16260 SARS-CoV-2_53_RIGHT_1 1 - GCAAAGAACACAAGCCCCAAC +MN908947.3 16112 16137 SARS-CoV-2_54_LEFT_1 2 + ACATGATGAGTTAACAGGACACATG +MN908947.3 16483 16508 SARS-CoV-2_54_RIGHT_1 2 - CCAAAAACTTGTCCATTAGCACACA +MN908947.3 16386 16408 SARS-CoV-2_55_LEFT_1 1 + AATGCTCCAGGTTGTGATGTCA +MN908947.3 16767 16796 SARS-CoV-2_55_RIGHT_1 1 - ACACGATAACCAGTAAAGACATAATTTCG +MN908947.3 16692 16714 SARS-CoV-2_56_LEFT_1 2 + ACTGTACGTGAAGTGCTGTCTG +MN908947.3 17082 17105 SARS-CoV-2_56_RIGHT_1 2 - TGACTCTTACCAGTACCAGGTGG +MN908947.3 16986 17013 SARS-CoV-2_57_LEFT_1 1 + GGCTTATACCCAACACTCAATATCTCA +MN908947.3 17381 17405 SARS-CoV-2_57_RIGHT_1 1 - CTGGCATTGACAACACTCAAATCA +MN908947.3 17323 17345 SARS-CoV-2_58_LEFT_1 2 + TGCCTGAGACGACAGCAGATAT +MN908947.3 17688 17711 SARS-CoV-2_58_RIGHT_1 2 - TGTGGCCTGTTAATTGCAGATGA +MN908947.3 17615 17642 SARS-CoV-2_59_LEFT_1 1 + GCTTAAAGCACATAAAGACAAATCAGC +MN908947.3 17997 18022 SARS-CoV-2_59_RIGHT_1 1 - TCCTACGTGGAATTTCAAGACTTGT +MN908947.3 17911 17939 SARS-CoV-2_60_LEFT_1 2 + ACAGATTTAATGTTGCTATTACCAGAGC +MN908947.3 18307 18328 SARS-CoV-2_60_RIGHT_1 2 - TAGCATGACACCCCTCGACAT +MN908947.3 18244 18267 SARS-CoV-2_61_LEFT_1 1 + ACCCTAACATGTTTATCACCCGC +MN908947.3 18624 18652 SARS-CoV-2_61_RIGHT_1 1 - GCTCAGGTCCTATTTTCACAAAATACTT +MN908947.3 18550 18578 SARS-CoV-2_62_LEFT_1 2 + GTGACACACTTAAAAATCTCTCTGACAG +MN908947.3 18936 18961 SARS-CoV-2_62_RIGHT_1 2 - CCGCATTAATCTTCAGTTCATCACC +MN908947.3 18869 18891 SARS-CoV-2_63_LEFT_1 1 + TAGGTGTCTAGCTGTCCACGAG +MN908947.3 19252 19277 SARS-CoV-2_63_RIGHT_1 1 - CCAGGCAAGTTAAGGTTAGATAGCA +MN908947.3 19183 19208 SARS-CoV-2_64_LEFT_1 2 + GCCTATTTTGGAATTGCAATGTCGA +MN908947.3 19558 19586 SARS-CoV-2_64_RIGHT_1 2 - GTATCAAATTGTTTGTAAACCCACAAGC +MN908947.3 19485 19513 SARS-CoV-2_65_LEFT_1 1 + GTCTGTAGACATCATGCTAATGAGTACA +MN908947.3 19877 19901 SARS-CoV-2_65_RIGHT_1 1 - GCTGGAGCATCTCTTTTGTAGTCC +MN908947.3 19810 19836 SARS-CoV-2_66_LEFT_1 2 + AACCAGTACCAGAGGTGAAAATACTC +MN908947.3 20186 20216 SARS-CoV-2_66_RIGHT_1 2 - TTTCTACTCTGAGTAAAGTAAGTTTCAGGT +MN908947.3 20090 20117 SARS-CoV-2_67_LEFT_1 1 + CAAACAAGCTAGTCTTAATGGAGTCAC +MN908947.3 20472 20497 SARS-CoV-2_67_RIGHT_1 1 - AACACACACACTTAGATGAACCTGT +MN908947.3 20377 20405 SARS-CoV-2_68_LEFT_1 2 + GACTAGCTAAACGTTTTAAGGAATCACC +MN908947.3 20766 20792 SARS-CoV-2_68_RIGHT_1 2 - GCGACATTCATCATTATGCCTTTAGG +MN908947.3 20677 20699 SARS-CoV-2_69_LEFT_1 1 + CGGGTGTTGCTATGCCTAATCT +MN908947.3 21050 21080 SARS-CoV-2_69_RIGHT_1 1 - TTTGTAACATTTTTAGTCTTAGGGTCGTAC +MN908947.3 20988 21013 SARS-CoV-2_70_LEFT_1 2 + TTGATTGGTGATTGTGCAACTGTAC +MN908947.3 21358 21387 SARS-CoV-2_70_RIGHT_1 2 - AGAATAGGAAGACAACTGAATTGGATTTG +MN908947.3 21294 21316 SARS-CoV-2_71_LEFT_1 1 + GGCAAACCACGCGAACAAATAG +MN908947.3 21675 21700 SARS-CoV-2_71_RIGHT_1 1 - TGAGGATCTGAAAACTTTGTCAGGG +MN908947.3 21532 21561 SARS-CoV-2_72_LEFT_1 2 + GTGATGTTCTTGTTAACAACTAAACGAAC +MN908947.3 21904 21933 SARS-CoV-2_72_RIGHT_1 2 - GTAGCGTTATTAACAATAAGTAGGGACTG +MN908947.3 21865 21889 SARS-CoV-2_73_LEFT_1 1 + AGAGGCTGGATTTTTGGTACTACT +MN908947.3 22247 22274 SARS-CoV-2_73_RIGHT_1 1 - ACCTAGTGATGTTAATACCTATTGGCA +MN908947.3 22091 22113 SARS-CoV-2_74_LEFT_1 2 + TGGACCTTGAAGGAAAACAGGG +MN908947.3 22474 22503 SARS-CoV-2_74_RIGHT_1 2 - TGATAGATTCCTTTTTCTACAGTGAAGGA +MN908947.3 22402 22428 SARS-CoV-2_75_LEFT_1 1 + GAAAATGGAACCATTACAGATGCTGT +MN908947.3 22785 22805 SARS-CoV-2_75_RIGHT_1 1 - TTTGCCCTGGAGCGATTTGT +MN908947.3 22648 22677 SARS-CoV-2_76_LEFT_2 2 + GCTGATTATTCTGTCCTATATAATTCCGC +MN908947.3 22742 22774 SARS-CoV-2_76_LEFT_1 2 + ATGTCTATGCAGATTCATTTGTAATTAGAGGT +MN908947.3 23028 23057 SARS-CoV-2_76_RIGHT_2 2 - GTTGGAAACCATATGATTGTAAAGGAAAG +MN908947.3 23120 23141 SARS-CoV-2_76_RIGHT_1 2 - GTCCACAAACAGTTGCTGGTG +MN908947.3 22944 22974 SARS-CoV-2_77_LEFT_1 1 + CAAACCTTTTGAGAGAGATATTTCAACTGA +MN908947.3 23327 23351 SARS-CoV-2_77_RIGHT_1 1 - CACTGACACCACCAAAAGAACATG +MN908947.3 23219 23246 SARS-CoV-2_78_LEFT_1 2 + CTGAGTCTAACAAAAAGTTTCTGCCTT +MN908947.3 23611 23635 SARS-CoV-2_78_RIGHT_1 2 - GGATTGACTAGCTACACTACGTGC +MN908947.3 23553 23575 SARS-CoV-2_79_LEFT_1 1 + ACCCATTGGTGCAGGTATATGC +MN908947.3 23914 23944 SARS-CoV-2_79_RIGHT_1 1 - AATTGGTGGTGTTTTGTAAATTTGTTTGAC +MN908947.3 23927 23955 SARS-CoV-2_79_RIGHT_2 1 - CCAAAATCTTTAATTGGTGGTGTTTTGT +MN908947.3 23853 23876 SARS-CoV-2_80_LEFT_1 2 + CCGTGCTTTAACTGGAATAGCTG +MN908947.3 24233 24258 SARS-CoV-2_80_RIGHT_1 2 - GCAAATGGTATTTGTAATGCAGCAC +MN908947.3 24171 24194 SARS-CoV-2_81_LEFT_1 1 + TGCTCAATACACTTCTGCACTGT +MN908947.3 24545 24567 SARS-CoV-2_81_RIGHT_1 1 - TGAAGTCTGCCTGTGATCAACC +MN908947.3 24426 24448 SARS-CoV-2_82_LEFT_1 2 + TGCACAAGCTTTAAACACGCTT +MN908947.3 24814 24836 SARS-CoV-2_82_RIGHT_1 2 - CACGAGGAAAGTGTGCTTTTCC +MN908947.3 24750 24772 SARS-CoV-2_83_LEFT_1 1 + GCATGTGACTTATGTCCCTGCA +MN908947.3 25122 25150 SARS-CoV-2_83_RIGHT_1 1 - AGATTCATTTAAATTCTTGGCAACCTCA +MN908947.3 25051 25076 SARS-CoV-2_84_LEFT_1 2 + GTTGATTTAGGTGACATCTCTGGCA +MN908947.3 25438 25461 SARS-CoV-2_84_RIGHT_1 2 - AGCATCCTTGATTTCACCTTGCT +MN908947.3 25331 25353 SARS-CoV-2_85_LEFT_1 1 + ATGAAGACGACTCTGAGCCAGT +MN908947.3 25711 25740 SARS-CoV-2_85_RIGHT_1 1 - CTGCAAGAAGTAGACTAAAGCATAAAGAT +MN908947.3 25645 25672 SARS-CoV-2_86_LEFT_1 2 + TGTTGTTTGTAACAGTTTACTCACACC +MN908947.3 26026 26050 SARS-CoV-2_86_RIGHT_1 2 - TCAATTGAGTTGAGTACAGCTGGT +MN908947.3 25951 25979 SARS-CoV-2_87_LEFT_1 1 + GTGGTTATACTGAAAAATGGGAATCTGG +MN908947.3 26338 26360 SARS-CoV-2_87_RIGHT_1 1 - AATCGAAGCGCAGTAAGGATGG +MN908947.3 26242 26268 SARS-CoV-2_88_LEFT_2 2 + TTATGTACTCATTCGTTTCGGAAGAG +MN908947.3 26255 26277 SARS-CoV-2_88_LEFT_1 2 + CGTTTCGGAAGAGACAGGTACG +MN908947.3 26635 26661 SARS-CoV-2_88_RIGHT_1 2 - ACAAAAACCTATTCCTGTTGGCATAG +MN908947.3 26564 26587 SARS-CoV-2_89_LEFT_1 1 + AAGCTCCTTGAACAATGGAACCT +MN908947.3 26592 26621 SARS-CoV-2_89_LEFT_2 1 + TAGGTTTCCTATTCCTTACATGGATTTGT +MN908947.3 26956 26979 SARS-CoV-2_89_RIGHT_1 1 - CAGCAATACGAAGATGTCCACGA +MN908947.3 26966 26991 SARS-CoV-2_89_RIGHT_2 1 - CTAGATGGTGTCCAGCAATACGAAG +MN908947.3 26873 26895 SARS-CoV-2_90_LEFT_1 2 + ATTCTTCTCAACGTGCCACTCC +MN908947.3 27218 27251 SARS-CoV-2_90_RIGHT_1 2 - ATTAGTAATATCTCTGCTATAGTAACCTGAAAG +MN908947.3 27256 27283 SARS-CoV-2_90_RIGHT_2 2 - TCCAAATGGAAACTTTAAAAGTCCTCA +MN908947.3 27152 27177 SARS-CoV-2_91_LEFT_1 1 + TCCAGTAGCAGTGACAATATTGCTT +MN908947.3 27534 27560 SARS-CoV-2_91_RIGHT_1 1 - AGTGCAAATTTGTTATCAGCTAGAGG +MN908947.3 27447 27473 SARS-CoV-2_92_LEFT_1 2 + CACTACCAAGAGTGTGTTAGAGGTAC +MN908947.3 27826 27855 SARS-CoV-2_92_RIGHT_1 2 - GTTCAAGTGAGAACCAAAAGATAATAAGC +MN908947.3 27700 27726 SARS-CoV-2_93_LEFT_1 1 + TTGTTGCGGCAATAGTGTTTATAACA +MN908947.3 28082 28104 SARS-CoV-2_93_RIGHT_1 1 - TGGGTGATTTAGAACCAGCCTC +MN908947.3 27996 28021 SARS-CoV-2_94_LEFT_1 2 + ACCCGTGTCCTATTCACTTCTATTC +MN908947.3 28394 28416 SARS-CoV-2_94_RIGHT_1 2 - TTATTGGGTAAACCTTGGGGCC +MN908947.3 28190 28214 SARS-CoV-2_95_LEFT_1 1 + GTGCGTTGTTCGTTCTATGAAGAC +MN908947.3 28572 28598 SARS-CoV-2_95_RIGHT_1 1 - ACCATCTTGGACTGAGATCTTTCATT +MN908947.3 28512 28536 SARS-CoV-2_96_LEFT_1 2 + AGATGACCAAATTGGCTACTACCG +MN908947.3 28893 28914 SARS-CoV-2_96_RIGHT_1 2 - CCATTGCCAGCCATTCTAGCA +MN908947.3 28827 28849 SARS-CoV-2_97_LEFT_1 1 + TTCCTCATCACGTAGTCGCAAC +MN908947.3 29206 29227 SARS-CoV-2_97_RIGHT_1 1 - CGACATTCCGAAGAACGCTGA +MN908947.3 29136 29161 SARS-CoV-2_98_LEFT_1 2 + CCAGGAACTAATCAGACAAGGAACT +MN908947.3 29512 29534 SARS-CoV-2_98_RIGHT_1 2 - TTTAGGCCTGAGTTGAGTCAGC +MN908947.3 29452 29475 SARS-CoV-2_99_LEFT_1 1 + CTTCTTCCTGCTGCAGATTTGGA +MN908947.3 29827 29854 SARS-CoV-2_99_RIGHT_1 1 - GCTATTAAAATCACATGGGGATAGCAC diff --git a/test/data/primer-schemes/artic/v4.1/reference.fasta b/test/data/bed-comment/reference.fasta similarity index 100% rename from test/data/primer-schemes/artic/v4.1/reference.fasta rename to test/data/bed-comment/reference.fasta diff --git a/test/data/broken/different-case/eden-v1-modified.primer.bed b/test/data/broken/different-case/eden-v1-modified.primer.bed deleted file mode 100644 index a74c002..0000000 --- a/test/data/broken/different-case/eden-v1-modified.primer.bed +++ /dev/null @@ -1,28 +0,0 @@ -MN908947.3 31 55 SARS2_A1F_31 1 + cCAACCAACTTTCGATCTCTTGTA -MN908947.3 2569 2593 SARS2_A1R_2569 1 - aGCTTCAACAGCTTCACTAGTAGG -MN908947.3 4295 4322 SARS2_A2F_4295 2 + cAGTGCTTAAAAAGTGTAAAAGTGCCT -MN908947.3 6847 6874 SARS2_A2R_6847 2 - aACAGTATTCTTTGCTATAGTAGTCGG -MN908947.3 8596 8620 SARS2_A3F_8596 1 + cTTGTGTTCCTTTTTGTTGCTGCT -MN908947.3 11049 11075 SARS2_A3R_11049 1 - aGAACAAAGACCATTGAGTACTCTGG -MN908947.3 12711 12733 SARS2_A4F_12711 2 + aCGACAGATGTCTTGTGCTGCC -MN908947.3 15225 15247 SARS2_A4R_15225 2 - tTAACATGTTGTGCCAACCACC -MN908947.3 16847 16872 SARS2_A5F_16847 1 + cTATGGTGATGCTGTTGTTTACCGA -MN908947.3 19254 19279 SARS2_A5R_19254 1 - aACCAGGCAAGTTAAGGTTAGATAG -MN908947.3 21358 21387 SARS2_A6F_21358 2 + cAAATCCAATTCAGTTGTCTTCCTATTCT -MN908947.3 23823 23848 SARS2_A6R_23823 2 - tTGTGTACAAAAACTGCCATATTGC -MN908947.3 25602 25624 SARS2_A7F_25602 1 + CTAGCACTCTCCAAGGGTGTTC -MN908947.3 28146 28173 SARS2_A7R_28146 1 - TAGGTTCCTGGCAATTAATTGTAAAAG -MN908947.3 1876 1898 SARS2_B1F_1876 2 + TCAGAGGCTGCTCGTGTTGTAC -MN908947.3 4429 4451 SARS2_B1R_4429 2 - TAGTTTCCACACAGACAGGCAT -MN908947.3 6287 6311 SARS2_B2F_6287 1 + GGTGTATACGTTGTCTTTGGAGCA -MN908947.3 8828 8852 SARS2_B2R_8828 1 - CCACTTCTCTTGTTATGACTGCAG -MN908947.3 10363 10385 SARS2_B3F_10363 2 + GTTCGCATTCAACCAGGACAGA -MN908947.3 12780 12803 SARS2_B3R_12780 2 - ACCTACCTCCCTTTGTTGTGTTG -MN908947.3 14546 14571 SARS2_B4F_14546 1 + GGAATTACTTGTGTATGCTGCTGAC -MN908947.3 17131 17153 SARS2_B4R_17131 1 - TACACTATGCGAGCAGAAGGGT -MN908947.3 18897 18919 SARS2_B5F_18897 2 + GTTAAGCGTGTTGACTGGACTA -MN908947.3 21428 21456 SARS2_B5R_21428 2 - TTGACCTTCTTTTAAAGACATAACAGCA -MN908947.3 23123 23145 SARS2_B6F_23123 1 + CAGCAACTGTTTGTGGACCTAA -MN908947.3 25647 25674 SARS2_B6R_25647 1 - AAGGTGTGAGTAAACTGTTACAAACAA -MN908947.3 27447 27472 SARS2_B7F_27447 2 + CACTACCAAGAGTGTGTTAGAGGTA -MN908947.3 29837 29867 SARS2_B7R_29837 2 - ATTCTCCTAAGAAGCTATTAAAATCACATG diff --git a/test/data/broken/different-case/eden-v1.primer.bed b/test/data/broken/different-case/eden-v1.primer.bed deleted file mode 100644 index 521b3ed..0000000 --- a/test/data/broken/different-case/eden-v1.primer.bed +++ /dev/null @@ -1,28 +0,0 @@ -MN908947.3 31 55 SARS2_A1F_31 1 + CCAACCAACTTTCGATCTCTTGTA -MN908947.3 2569 2593 SARS2_A1R_2569 1 - AGCTTCAACAGCTTCACTAGTAGG -MN908947.3 4295 4322 SARS2_A2F_4295 2 + CAGTGCTTAAAAAGTGTAAAAGTGCCT -MN908947.3 6847 6874 SARS2_A2R_6847 2 - AACAGTATTCTTTGCTATAGTAGTCGG -MN908947.3 8596 8620 SARS2_A3F_8596 1 + CTTGTGTTCCTTTTTGTTGCTGCT -MN908947.3 11049 11075 SARS2_A3R_11049 1 - AGAACAAAGACCATTGAGTACTCTGG -MN908947.3 12711 12733 SARS2_A4F_12711 2 + ACGACAGATGTCTTGTGCTGCC -MN908947.3 15225 15247 SARS2_A4R_15225 2 - TTAACATGTTGTGCCAACCACC -MN908947.3 16847 16872 SARS2_A5F_16847 1 + CTATGGTGATGCTGTTGTTTACCGA -MN908947.3 19254 19279 SARS2_A5R_19254 1 - AACCAGGCAAGTTAAGGTTAGATAG -MN908947.3 21358 21387 SARS2_A6F_21358 2 + CAAATCCAATTCAGTTGTCTTCCTATTCT -MN908947.3 23823 23848 SARS2_A6R_23823 2 - TTGTGTACAAAAACTGCCATATTGC -MN908947.3 25602 25624 SARS2_A7F_25602 1 + CTAGCACTCTCCAAGGGTGTTC -MN908947.3 28146 28173 SARS2_A7R_28146 1 - TAGGTTCCTGGCAATTAATTGTAAAAG -MN908947.3 1876 1898 SARS2_B1F_1876 2 + TCAGAGGCTGCTCGTGTTGTAC -MN908947.3 4429 4451 SARS2_B1R_4429 2 - TAGTTTCCACACAGACAGGCAT -MN908947.3 6287 6311 SARS2_B2F_6287 1 + GGTGTATACGTTGTCTTTGGAGCA -MN908947.3 8828 8852 SARS2_B2R_8828 1 - CCACTTCTCTTGTTATGACTGCAG -MN908947.3 10363 10385 SARS2_B3F_10363 2 + GTTCGCATTCAACCAGGACAGA -MN908947.3 12780 12803 SARS2_B3R_12780 2 - ACCTACCTCCCTTTGTTGTGTTG -MN908947.3 14546 14571 SARS2_B4F_14546 1 + GGAATTACTTGTGTATGCTGCTGAC -MN908947.3 17131 17153 SARS2_B4R_17131 1 - TACACTATGCGAGCAGAAGGGT -MN908947.3 18897 18919 SARS2_B5F_18897 2 + GTTAAGCGTGTTGACTGGACTA -MN908947.3 21428 21456 SARS2_B5R_21428 2 - TTGACCTTCTTTTAAAGACATAACAGCA -MN908947.3 23123 23145 SARS2_B6F_23123 1 + CAGCAACTGTTTGTGGACCTAA -MN908947.3 25647 25674 SARS2_B6R_25647 1 - AAGGTGTGAGTAAACTGTTACAAACAA -MN908947.3 27447 27472 SARS2_B7F_27447 2 + CACTACCAAGAGTGTGTTAGAGGTA -MN908947.3 29837 29867 SARS2_B7R_29837 2 - ATTCTCCTAAGAAGCTATTAAAATCACATG diff --git a/test/data/broken/duplicated-primers/info.yml b/test/data/broken/duplicated-primers/info.yml new file mode 100644 index 0000000..133ad6c --- /dev/null +++ b/test/data/broken/duplicated-primers/info.yml @@ -0,0 +1,20 @@ +schema_version: 1.0.0-alpha +name: eden +amplicon_size: 2500 +version: v1 +organism: sars-cov-2 +aliases: +- sydney +developers: +- John-Sebastian Eden +- Eby Sim +definition_url: https://github.com/pha4ge/primer-schemes/tree/main/sars-cov-2/eden/v1 +citations: +- https://www.protocols.io/view/sars-cov-2-genome-sequencing-using-long-pooled-amp-kxygxeob4v8j/v1 +notes: +- Protocol includes addendum for ONT sequencing +license: CC-BY-4.0 +citations: + - https://dx.doi.org/10.17504/protocols.io.befyjbpw +primer_checksum: primaschema:55c9726eb1400cab +reference_checksum: primaschema:b1acd7163146bf17 diff --git a/test/data/broken/duplicated-primers/primer.bed b/test/data/broken/duplicated-primers/primer.bed new file mode 100644 index 0000000..3b5502d --- /dev/null +++ b/test/data/broken/duplicated-primers/primer.bed @@ -0,0 +1,5 @@ +MN908947.3 31 55 SARS2_1_LEFT_1 1 + CCAACCAACTTTCGATCTCTTGTA +MN908947.3 2569 2593 SARS2_1_RIGHT_1 1 - AGCTTCAACAGCTTCACTAGTAGG +MN908947.3 1876 1898 SARS2_2_LEFT_1 2 + TCAGAGGCTGCTCGTGTTGTAC +MN908947.3 4429 4451 SARS2_2_RIGHT_1 2 - TAGTTTCCACACAGACAGGCAT +MN908947.3 4429 4451 SARS2_2_RIGHT_1 2 - TAGTTTCCACACAGACAGGCAT diff --git a/test/data/primer-schemes/eden/v1/reference.fasta b/test/data/broken/duplicated-primers/reference.fasta similarity index 100% rename from test/data/primer-schemes/eden/v1/reference.fasta rename to test/data/broken/duplicated-primers/reference.fasta diff --git a/test/data/broken/end-before-start/info.yml b/test/data/broken/end-before-start/info.yml new file mode 100644 index 0000000..07a1c73 --- /dev/null +++ b/test/data/broken/end-before-start/info.yml @@ -0,0 +1,20 @@ +schema_version: 1.0.0-alpha +name: eden +amplicon_size: 2500 +version: v1 +organism: sars-cov-2 +aliases: +- sydney +developers: +- John-Sebastian Eden +- Eby Sim +definition_url: https://github.com/pha4ge/primer-schemes/tree/main/sars-cov-2/eden/v1 +citations: +- https://www.protocols.io/view/sars-cov-2-genome-sequencing-using-long-pooled-amp-kxygxeob4v8j/v1 +notes: +- Protocol includes addendum for ONT sequencing +license: CC-BY-4.0 +citations: + - https://dx.doi.org/10.17504/protocols.io.befyjbpw +primer_checksum: primaschema:5bfc602ebd6526a8 +reference_checksum: primaschema:b1acd7163146bf17 diff --git a/test/data/broken/end-before-start/primer.bed b/test/data/broken/end-before-start/primer.bed new file mode 100644 index 0000000..557d5b6 --- /dev/null +++ b/test/data/broken/end-before-start/primer.bed @@ -0,0 +1,4 @@ +MN908947.3 2569 2593 SARS2_1_LEFT_1 1 - AGCTTCAACAGCTTCACTAGTAGG +MN908947.3 31 55 SARS2_1_RIGHT_1 1 + CCAACCAACTTTCGATCTCTTGTA +MN908947.3 1876 1898 SARS2_2_LEFT_1 2 + TCAGAGGCTGCTCGTGTTGTAC +MN908947.3 4429 4451 SARS2_2_RIGHT_1 2 - TAGTTTCCACACAGACAGGCAT diff --git a/test/data/broken/end-before-start/reference.fasta b/test/data/broken/end-before-start/reference.fasta new file mode 100644 index 0000000..e1cfd92 --- /dev/null +++ b/test/data/broken/end-before-start/reference.fasta @@ -0,0 +1,429 @@ +>MN908947.3 +ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAA +CGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAAC +TAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTG +TTGCAGCCGATCATCAGCACATCTAGGTTTCGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTC +CCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTAC +GTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGG +CTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAAACGTTCGGAT +GCTCGAACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACTCGAAGGCATTCAGTACGGTC +GTAGTGGTGAGACACTTGGTGTCCTTGTCCCTCATGTGGGCGAAATACCAGTGGCTTACCGCAAGGTTCT +TCTTCGTAAGAACGGTAATAAAGGAGCTGGTGGCCATAGTTACGGCGCCGATCTAAAGTCATTTGACTTA +GGCGACGAGCTTGGCACTGATCCTTATGAAGATTTTCAAGAAAACTGGAACACTAAACATAGCAGTGGTG +TTACCCGTGAACTCATGCGTGAGCTTAACGGAGGGGCATACACTCGCTATGTCGATAACAACTTCTGTGG +CCCTGATGGCTACCCTCTTGAGTGCATTAAAGACCTTCTAGCACGTGCTGGTAAAGCTTCATGCACTTTG +TCCGAACAACTGGACTTTATTGACACTAAGAGGGGTGTATACTGCTGCCGTGAACATGAGCATGAAATTG +CTTGGTACACGGAACGTTCTGAAAAGAGCTATGAATTGCAGACACCTTTTGAAATTAAATTGGCAAAGAA +ATTTGACACCTTCAATGGGGAATGTCCAAATTTTGTATTTCCCTTAAATTCCATAATCAAGACTATTCAA +CCAAGGGTTGAAAAGAAAAAGCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCCAGTTGCGTCAC +CAAATGAATGCAACCAAATGTGCCTTTCAACTCTCATGAAGTGTGATCATTGTGGTGAAACTTCATGGCA +GACGGGCGATTTTGTTAAAGCCACTTGCGAATTTTGTGGCACTGAGAATTTGACTAAAGAAGGTGCCACT +ACTTGTGGTTACTTACCCCAAAATGCTGTTGTTAAAATTTATTGTCCAGCATGTCACAATTCAGAAGTAG +GACCTGAGCATAGTCTTGCCGAATACCATAATGAATCTGGCTTGAAAACCATTCTTCGTAAGGGTGGTCG +CACTATTGCCTTTGGAGGCTGTGTGTTCTCTTATGTTGGTTGCCATAACAAGTGTGCCTATTGGGTTCCA +CGTGCTAGCGCTAACATAGGTTGTAACCATACAGGTGTTGTTGGAGAAGGTTCCGAAGGTCTTAATGACA +ACCTTCTTGAAATACTCCAAAAAGAGAAAGTCAACATCAATATTGTTGGTGACTTTAAACTTAATGAAGA +GATCGCCATTATTTTGGCATCTTTTTCTGCTTCCACAAGTGCTTTTGTGGAAACTGTGAAAGGTTTGGAT +TATAAAGCATTCAAACAAATTGTTGAATCCTGTGGTAATTTTAAAGTTACAAAAGGAAAAGCTAAAAAAG +GTGCCTGGAATATTGGTGAACAGAAATCAATACTGAGTCCTCTTTATGCATTTGCATCAGAGGCTGCTCG +TGTTGTACGATCAATTTTCTCCCGCACTCTTGAAACTGCTCAAAATTCTGTGCGTGTTTTACAGAAGGCC +GCTATAACAATACTAGATGGAATTTCACAGTATTCACTGAGACTCATTGATGCTATGATGTTCACATCTG +ATTTGGCTACTAACAATCTAGTTGTAATGGCCTACATTACAGGTGGTGTTGTTCAGTTGACTTCGCAGTG +GCTAACTAACATCTTTGGCACTGTTTATGAAAAACTCAAACCCGTCCTTGATTGGCTTGAAGAGAAGTTT +AAGGAAGGTGTAGAGTTTCTTAGAGACGGTTGGGAAATTGTTAAATTTATCTCAACCTGTGCTTGTGAAA +TTGTCGGTGGACAAATTGTCACCTGTGCAAAGGAAATTAAGGAGAGTGTTCAGACATTCTTTAAGCTTGT +AAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGCCTTGAATTTA +GGTGAAACATTTGTCACGCACTCAAAGGGATTGTACAGAAAGTGTGTTAAATCCAGAGAAGAAACTGGCC +TACTCATGCCTCTAAAAGCCCCAAAAGAAATTATCTTCTTAGAGGGAGAAACACTTCCCACAGAAGTGTT +AACAGAGGAAGTTGTCTTGAAAACTGGTGATTTACAACCATTAGAACAACCTACTAGTGAAGCTGTTGAA +GCTCCATTGGTTGGTACACCAGTTTGTATTAACGGGCTTATGTTGCTCGAAATCAAAGACACAGAAAAGT +ACTGTGCCCTTGCACCTAATATGATGGTAACAAACAATACCTTCACACTCAAAGGCGGTGCACCAACAAA +GGTTACTTTTGGTGATGACACTGTGATAGAAGTGCAAGGTTACAAGAGTGTGAATATCACTTTTGAACTT +GATGAAAGGATTGATAAAGTACTTAATGAGAAGTGCTCTGCCTATACAGTTGAACTCGGTACAGAAGTAA +ATGAGTTCGCCTGTGTTGTGGCAGATGCTGTCATAAAAACTTTGCAACCAGTATCTGAATTACTTACACC +ACTGGGCATTGATTTAGATGAGTGGAGTATGGCTACATACTACTTATTTGATGAGTCTGGTGAGTTTAAA +TTGGCTTCACATATGTATTGTTCTTTCTACCCTCCAGATGAGGATGAAGAAGAAGGTGATTGTGAAGAAG +AAGAGTTTGAGCCATCAACTCAATATGAGTATGGTACTGAAGATGATTACCAAGGTAAACCTTTGGAATT +TGGTGCCACTTCTGCTGCTCTTCAACCTGAAGAAGAGCAAGAAGAAGATTGGTTAGATGATGATAGTCAA +CAAACTGTTGGTCAACAAGACGGCAGTGAGGACAATCAGACAACTACTATTCAAACAATTGTTGAGGTTC +AACCTCAATTAGAGATGGAACTTACACCAGTTGTTCAGACTATTGAAGTGAATAGTTTTAGTGGTTATTT +AAAACTTACTGACAATGTATACATTAAAAATGCAGACATTGTGGAAGAAGCTAAAAAGGTAAAACCAACA +GTGGTTGTTAATGCAGCCAATGTTTACCTTAAACATGGAGGAGGTGTTGCAGGAGCCTTAAATAAGGCTA +CTAACAATGCCATGCAAGTTGAATCTGATGATTACATAGCTACTAATGGACCACTTAAAGTGGGTGGTAG +TTGTGTTTTAAGCGGACACAATCTTGCTAAACACTGTCTTCATGTTGTCGGCCCAAATGTTAACAAAGGT +GAAGACATTCAACTTCTTAAGAGTGCTTATGAAAATTTTAATCAGCACGAAGTTCTACTTGCACCATTAT +TATCAGCTGGTATTTTTGGTGCTGACCCTATACATTCTTTAAGAGTTTGTGTAGATACTGTTCGCACAAA +TGTCTACTTAGCTGTCTTTGATAAAAATCTCTATGACAAACTTGTTTCAAGCTTTTTGGAAATGAAGAGT +GAAAAGCAAGTTGAACAAAAGATCGCTGAGATTCCTAAAGAGGAAGTTAAGCCATTTATAACTGAAAGTA +AACCTTCAGTTGAACAGAGAAAACAAGATGATAAGAAAATCAAAGCTTGTGTTGAAGAAGTTACAACAAC +TCTGGAAGAAACTAAGTTCCTCACAGAAAACTTGTTACTTTATATTGACATTAATGGCAATCTTCATCCA +GATTCTGCCACTCTTGTTAGTGACATTGACATCACTTTCTTAAAGAAAGATGCTCCATATATAGTGGGTG +ATGTTGTTCAAGAGGGTGTTTTAACTGCTGTGGTTATACCTACTAAAAAGGCTGGTGGCACTACTGAAAT +GCTAGCGAAAGCTTTGAGAAAAGTGCCAACAGACAATTATATAACCACTTACCCGGGTCAGGGTTTAAAT +GGTTACACTGTAGAGGAGGCAAAGACAGTGCTTAAAAAGTGTAAAAGTGCCTTTTACATTCTACCATCTA +TTATCTCTAATGAGAAGCAAGAAATTCTTGGAACTGTTTCTTGGAATTTGCGAGAAATGCTTGCACATGC +AGAAGAAACACGCAAATTAATGCCTGTCTGTGTGGAAACTAAAGCCATAGTTTCAACTATACAGCGTAAA +TATAAGGGTATTAAAATACAAGAGGGTGTGGTTGATTATGGTGCTAGATTTTACTTTTACACCAGTAAAA +CAACTGTAGCGTCACTTATCAACACACTTAACGATCTAAATGAAACTCTTGTTACAATGCCACTTGGCTA +TGTAACACATGGCTTAAATTTGGAAGAAGCTGCTCGGTATATGAGATCTCTCAAAGTGCCAGCTACAGTT +TCTGTTTCTTCACCTGATGCTGTTACAGCGTATAATGGTTATCTTACTTCTTCTTCTAAAACACCTGAAG +AACATTTTATTGAAACCATCTCACTTGCTGGTTCCTATAAAGATTGGTCCTATTCTGGACAATCTACACA +ACTAGGTATAGAATTTCTTAAGAGAGGTGATAAAAGTGTATATTACACTAGTAATCCTACCACATTCCAC +CTAGATGGTGAAGTTATCACCTTTGACAATCTTAAGACACTTCTTTCTTTGAGAGAAGTGAGGACTATTA +AGGTGTTTACAACAGTAGACAACATTAACCTCCACACGCAAGTTGTGGACATGTCAATGACATATGGACA +ACAGTTTGGTCCAACTTATTTGGATGGAGCTGATGTTACTAAAATAAAACCTCATAATTCACATGAAGGT +AAAACATTTTATGTTTTACCTAATGATGACACTCTACGTGTTGAGGCTTTTGAGTACTACCACACAACTG +ATCCTAGTTTTCTGGGTAGGTACATGTCAGCATTAAATCACACTAAAAAGTGGAAATACCCACAAGTTAA +TGGTTTAACTTCTATTAAATGGGCAGATAACAACTGTTATCTTGCCACTGCATTGTTAACACTCCAACAA +ATAGAGTTGAAGTTTAATCCACCTGCTCTACAAGATGCTTATTACAGAGCAAGGGCTGGTGAAGCTGCTA +ACTTTTGTGCACTTATCTTAGCCTACTGTAATAAGACAGTAGGTGAGTTAGGTGATGTTAGAGAAACAAT +GAGTTACTTGTTTCAACATGCCAATTTAGATTCTTGCAAAAGAGTCTTGAACGTGGTGTGTAAAACTTGT +GGACAACAGCAGACAACCCTTAAGGGTGTAGAAGCTGTTATGTACATGGGCACACTTTCTTATGAACAAT +TTAAGAAAGGTGTTCAGATACCTTGTACGTGTGGTAAACAAGCTACAAAATATCTAGTACAACAGGAGTC +ACCTTTTGTTATGATGTCAGCACCACCTGCTCAGTATGAACTTAAGCATGGTACATTTACTTGTGCTAGT +GAGTACACTGGTAATTACCAGTGTGGTCACTATAAACATATAACTTCTAAAGAAACTTTGTATTGCATAG +ACGGTGCTTTACTTACAAAGTCCTCAGAATACAAAGGTCCTATTACGGATGTTTTCTACAAAGAAAACAG +TTACACAACAACCATAAAACCAGTTACTTATAAATTGGATGGTGTTGTTTGTACAGAAATTGACCCTAAG +TTGGACAATTATTATAAGAAAGACAATTCTTATTTCACAGAGCAACCAATTGATCTTGTACCAAACCAAC +CATATCCAAACGCAAGCTTCGATAATTTTAAGTTTGTATGTGATAATATCAAATTTGCTGATGATTTAAA +CCAGTTAACTGGTTATAAGAAACCTGCTTCAAGAGAGCTTAAAGTTACATTTTTCCCTGACTTAAATGGT +GATGTGGTGGCTATTGATTATAAACACTACACACCCTCTTTTAAGAAAGGAGCTAAATTGTTACATAAAC +CTATTGTTTGGCATGTTAACAATGCAACTAATAAAGCCACGTATAAACCAAATACCTGGTGTATACGTTG +TCTTTGGAGCACAAAACCAGTTGAAACATCAAATTCGTTTGATGTACTGAAGTCAGAGGACGCGCAGGGA +ATGGATAATCTTGCCTGCGAAGATCTAAAACCAGTCTCTGAAGAAGTAGTGGAAAATCCTACCATACAGA +AAGACGTTCTTGAGTGTAATGTGAAAACTACCGAAGTTGTAGGAGACATTATACTTAAACCAGCAAATAA +TAGTTTAAAAATTACAGAAGAGGTTGGCCACACAGATCTAATGGCTGCTTATGTAGACAATTCTAGTCTT +ACTATTAAGAAACCTAATGAATTATCTAGAGTATTAGGTTTGAAAACCCTTGCTACTCATGGTTTAGCTG +CTGTTAATAGTGTCCCTTGGGATACTATAGCTAATTATGCTAAGCCTTTTCTTAACAAAGTTGTTAGTAC +AACTACTAACATAGTTACACGGTGTTTAAACCGTGTTTGTACTAATTATATGCCTTATTTCTTTACTTTA +TTGCTACAATTGTGTACTTTTACTAGAAGTACAAATTCTAGAATTAAAGCATCTATGCCGACTACTATAG +CAAAGAATACTGTTAAGAGTGTCGGTAAATTTTGTCTAGAGGCTTCATTTAATTATTTGAAGTCACCTAA +TTTTTCTAAACTGATAAATATTATAATTTGGTTTTTACTATTAAGTGTTTGCCTAGGTTCTTTAATCTAC +TCAACCGCTGCTTTAGGTGTTTTAATGTCTAATTTAGGCATGCCTTCTTACTGTACTGGTTACAGAGAAG +GCTATTTGAACTCTACTAATGTCACTATTGCAACCTACTGTACTGGTTCTATACCTTGTAGTGTTTGTCT +TAGTGGTTTAGATTCTTTAGACACCTATCCTTCTTTAGAAACTATACAAATTACCATTTCATCTTTTAAA +TGGGATTTAACTGCTTTTGGCTTAGTTGCAGAGTGGTTTTTGGCATATATTCTTTTCACTAGGTTTTTCT +ATGTACTTGGATTGGCTGCAATCATGCAATTGTTTTTCAGCTATTTTGCAGTACATTTTATTAGTAATTC +TTGGCTTATGTGGTTAATAATTAATCTTGTACAAATGGCCCCGATTTCAGCTATGGTTAGAATGTACATC +TTCTTTGCATCATTTTATTATGTATGGAAAAGTTATGTGCATGTTGTAGACGGTTGTAATTCATCAACTT +GTATGATGTGTTACAAACGTAATAGAGCAACAAGAGTCGAATGTACAACTATTGTTAATGGTGTTAGAAG +GTCCTTTTATGTCTATGCTAATGGAGGTAAAGGCTTTTGCAAACTACACAATTGGAATTGTGTTAATTGT +GATACATTCTGTGCTGGTAGTACATTTATTAGTGATGAAGTTGCGAGAGACTTGTCACTACAGTTTAAAA +GACCAATAAATCCTACTGACCAGTCTTCTTACATCGTTGATAGTGTTACAGTGAAGAATGGTTCCATCCA +TCTTTACTTTGATAAAGCTGGTCAAAAGACTTATGAAAGACATTCTCTCTCTCATTTTGTTAACTTAGAC +AACCTGAGAGCTAATAACACTAAAGGTTCATTGCCTATTAATGTTATAGTTTTTGATGGTAAATCAAAAT +GTGAAGAATCATCTGCAAAATCAGCGTCTGTTTACTACAGTCAGCTTATGTGTCAACCTATACTGTTACT +AGATCAGGCATTAGTGTCTGATGTTGGTGATAGTGCGGAAGTTGCAGTTAAAATGTTTGATGCTTACGTT +AATACGTTTTCATCAACTTTTAACGTACCAATGGAAAAACTCAAAACACTAGTTGCAACTGCAGAAGCTG +AACTTGCAAAGAATGTGTCCTTAGACAATGTCTTATCTACTTTTATTTCAGCAGCTCGGCAAGGGTTTGT +TGATTCAGATGTAGAAACTAAAGATGTTGTTGAATGTCTTAAATTGTCACATCAATCTGACATAGAAGTT +ACTGGCGATAGTTGTAATAACTATATGCTCACCTATAACAAAGTTGAAAACATGACACCCCGTGACCTTG +GTGCTTGTATTGACTGTAGTGCGCGTCATATTAATGCGCAGGTAGCAAAAAGTCACAACATTGCTTTGAT +ATGGAACGTTAAAGATTTCATGTCATTGTCTGAACAACTACGAAAACAAATACGTAGTGCTGCTAAAAAG +AATAACTTACCTTTTAAGTTGACATGTGCAACTACTAGACAAGTTGTTAATGTTGTAACAACAAAGATAG +CACTTAAGGGTGGTAAAATTGTTAATAATTGGTTGAAGCAGTTAATTAAAGTTACACTTGTGTTCCTTTT +TGTTGCTGCTATTTTCTATTTAATAACACCTGTTCATGTCATGTCTAAACATACTGACTTTTCAAGTGAA +ATCATAGGATACAAGGCTATTGATGGTGGTGTCACTCGTGACATAGCATCTACAGATACTTGTTTTGCTA +ACAAACATGCTGATTTTGACACATGGTTTAGCCAGCGTGGTGGTAGTTATACTAATGACAAAGCTTGCCC +ATTGATTGCTGCAGTCATAACAAGAGAAGTGGGTTTTGTCGTGCCTGGTTTGCCTGGCACGATATTACGC +ACAACTAATGGTGACTTTTTGCATTTCTTACCTAGAGTTTTTAGTGCAGTTGGTAACATCTGTTACACAC +CATCAAAACTTATAGAGTACACTGACTTTGCAACATCAGCTTGTGTTTTGGCTGCTGAATGTACAATTTT +TAAAGATGCTTCTGGTAAGCCAGTACCATATTGTTATGATACCAATGTACTAGAAGGTTCTGTTGCTTAT +GAAAGTTTACGCCCTGACACACGTTATGTGCTCATGGATGGCTCTATTATTCAATTTCCTAACACCTACC +TTGAAGGTTCTGTTAGAGTGGTAACAACTTTTGATTCTGAGTACTGTAGGCACGGCACTTGTGAAAGATC +AGAAGCTGGTGTTTGTGTATCTACTAGTGGTAGATGGGTACTTAACAATGATTATTACAGATCTTTACCA +GGAGTTTTCTGTGGTGTAGATGCTGTAAATTTACTTACTAATATGTTTACACCACTAATTCAACCTATTG +GTGCTTTGGACATATCAGCATCTATAGTAGCTGGTGGTATTGTAGCTATCGTAGTAACATGCCTTGCCTA +CTATTTTATGAGGTTTAGAAGAGCTTTTGGTGAATACAGTCATGTAGTTGCCTTTAATACTTTACTATTC +CTTATGTCATTCACTGTACTCTGTTTAACACCAGTTTACTCATTCTTACCTGGTGTTTATTCTGTTATTT +ACTTGTACTTGACATTTTATCTTACTAATGATGTTTCTTTTTTAGCACATATTCAGTGGATGGTTATGTT +CACACCTTTAGTACCTTTCTGGATAACAATTGCTTATATCATTTGTATTTCCACAAAGCATTTCTATTGG +TTCTTTAGTAATTACCTAAAGAGACGTGTAGTCTTTAATGGTGTTTCCTTTAGTACTTTTGAAGAAGCTG +CGCTGTGCACCTTTTTGTTAAATAAAGAAATGTATCTAAAGTTGCGTAGTGATGTGCTATTACCTCTTAC +GCAATATAATAGATACTTAGCTCTTTATAATAAGTACAAGTATTTTAGTGGAGCAATGGATACAACTAGC +TACAGAGAAGCTGCTTGTTGTCATCTCGCAAAGGCTCTCAATGACTTCAGTAACTCAGGTTCTGATGTTC +TTTACCAACCACCACAAACCTCTATCACCTCAGCTGTTTTGCAGAGTGGTTTTAGAAAAATGGCATTCCC +ATCTGGTAAAGTTGAGGGTTGTATGGTACAAGTAACTTGTGGTACAACTACACTTAACGGTCTTTGGCTT +GATGACGTAGTTTACTGTCCAAGACATGTGATCTGCACCTCTGAAGACATGCTTAACCCTAATTATGAAG +ATTTACTCATTCGTAAGTCTAATCATAATTTCTTGGTACAGGCTGGTAATGTTCAACTCAGGGTTATTGG +ACATTCTATGCAAAATTGTGTACTTAAGCTTAAGGTTGATACAGCCAATCCTAAGACACCTAAGTATAAG +TTTGTTCGCATTCAACCAGGACAGACTTTTTCAGTGTTAGCTTGTTACAATGGTTCACCATCTGGTGTTT +ACCAATGTGCTATGAGGCCCAATTTCACTATTAAGGGTTCATTCCTTAATGGTTCATGTGGTAGTGTTGG +TTTTAACATAGATTATGACTGTGTCTCTTTTTGTTACATGCACCATATGGAATTACCAACTGGAGTTCAT +GCTGGCACAGACTTAGAAGGTAACTTTTATGGACCTTTTGTTGACAGGCAAACAGCACAAGCAGCTGGTA +CGGACACAACTATTACAGTTAATGTTTTAGCTTGGTTGTACGCTGCTGTTATAAATGGAGACAGGTGGTT +TCTCAATCGATTTACCACAACTCTTAATGACTTTAACCTTGTGGCTATGAAGTACAATTATGAACCTCTA +ACACAAGACCATGTTGACATACTAGGACCTCTTTCTGCTCAAACTGGAATTGCCGTTTTAGATATGTGTG +CTTCATTAAAAGAATTACTGCAAAATGGTATGAATGGACGTACCATATTGGGTAGTGCTTTATTAGAAGA +TGAATTTACACCTTTTGATGTTGTTAGACAATGCTCAGGTGTTACTTTCCAAAGTGCAGTGAAAAGAACA +ATCAAGGGTACACACCACTGGTTGTTACTCACAATTTTGACTTCACTTTTAGTTTTAGTCCAGAGTACTC +AATGGTCTTTGTTCTTTTTTTTGTATGAAAATGCCTTTTTACCTTTTGCTATGGGTATTATTGCTATGTC +TGCTTTTGCAATGATGTTTGTCAAACATAAGCATGCATTTCTCTGTTTGTTTTTGTTACCTTCTCTTGCC +ACTGTAGCTTATTTTAATATGGTCTATATGCCTGCTAGTTGGGTGATGCGTATTATGACATGGTTGGATA +TGGTTGATACTAGTTTGTCTGGTTTTAAGCTAAAAGACTGTGTTATGTATGCATCAGCTGTAGTGTTACT +AATCCTTATGACAGCAAGAACTGTGTATGATGATGGTGCTAGGAGAGTGTGGACACTTATGAATGTCTTG +ACACTCGTTTATAAAGTTTATTATGGTAATGCTTTAGATCAAGCCATTTCCATGTGGGCTCTTATAATCT +CTGTTACTTCTAACTACTCAGGTGTAGTTACAACTGTCATGTTTTTGGCCAGAGGTATTGTTTTTATGTG +TGTTGAGTATTGCCCTATTTTCTTCATAACTGGTAATACACTTCAGTGTATAATGCTAGTTTATTGTTTC +TTAGGCTATTTTTGTACTTGTTACTTTGGCCTCTTTTGTTTACTCAACCGCTACTTTAGACTGACTCTTG +GTGTTTATGATTACTTAGTTTCTACACAGGAGTTTAGATATATGAATTCACAGGGACTACTCCCACCCAA +GAATAGCATAGATGCCTTCAAACTCAACATTAAATTGTTGGGTGTTGGTGGCAAACCTTGTATCAAAGTA +GCCACTGTACAGTCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAAC +TCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAA +AGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTA +GACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAAGCTATAGCCTCAGAGTTTA +GTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGA +TTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCA +GCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTG +AGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAA +TGATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACA +ACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACAT +TTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAG +TGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCT +GCTGTCAAATTACAGAATAATGAGCTTAGTCCTGTTGCACTACGACAGATGTCTTGTGCTGCCGGTACTA +CACAAACTGCTTGCACTGATGACAATGCGTTAGCTTACTACAACACAACAAAGGGAGGTAGGTTTGTACT +TGCACTGTTATCCGATTTACAGGATTTGAAATGGGCTAGATTCCCTAAGAGTGATGGAACTGGTACTATC +TATACAGAACTGGAACCACCTTGTAGGTTTGTTACAGACACACCTAAAGGTCCTAAAGTGAAGTATTTAT +ACTTTATTAAAGGATTAAACAACCTAAATAGAGGTATGGTACTTGGTAGTTTAGCTGCCACAGTACGTCT +ACAAGCTGGTAATGCAACAGAAGTGCCTGCCAATTCAACTGTATTATCTTTCTGTGCTTTTGCTGTAGAT +GCTGCTAAAGCTTACAAAGATTATCTAGCTAGTGGGGGACAACCAATCACTAATTGTGTTAAGATGTTGT +GTACACACACTGGTACTGGTCAGGCAATAACAGTTACACCGGAAGCCAATATGGATCAAGAATCCTTTGG +TGGTGCATCGTGTTGTCTGTACTGCCGTTGCCACATAGATCATCCAAATCCTAAAGGATTTTGTGACTTA +AAAGGTAAGTATGTACAAATACCTACAACTTGTGCTAATGACCCTGTGGGTTTTACACTTAAAAACACAG +TCTGTACCGTCTGCGGTATGTGGAAAGGTTATGGCTGTAGTTGTGATCAACTCCGCGAACCCATGCTTCA +GTCAGCTGATGCACAATCGTTTTTAAACGGGTTTGCGGTGTAAGTGCAGCCCGTCTTACACCGTGCGGCA +CAGGCACTAGTACTGATGTCGTATACAGGGCTTTTGACATCTACAATGATAAAGTAGCTGGTTTTGCTAA +ATTCCTAAAAACTAATTGTTGTCGCTTCCAAGAAAAGGACGAAGATGACAATTTAATTGATTCTTACTTT +GTAGTTAAGAGACACACTTTCTCTAACTACCAACATGAAGAAACAATTTATAATTTACTTAAGGATTGTC +CAGCTGTTGCTAAACATGACTTCTTTAAGTTTAGAATAGACGGTGACATGGTACCACATATATCACGTCA +ACGTCTTACTAAATACACAATGGCAGACCTCGTCTATGCTTTAAGGCATTTTGATGAAGGTAATTGTGAC +ACATTAAAAGAAATACTTGTCACATACAATTGTTGTGATGATGATTATTTCAATAAAAAGGACTGGTATG +ATTTTGTAGAAAACCCAGATATATTACGCGTATACGCCAACTTAGGTGAACGTGTACGCCAAGCTTTGTT +AAAAACAGTACAATTCTGTGATGCCATGCGAAATGCTGGTATTGTTGGTGTACTGACATTAGATAATCAA +GATCTCAATGGTAACTGGTATGATTTCGGTGATTTCATACAAACCACGCCAGGTAGTGGAGTTCCTGTTG +TAGATTCTTATTATTCATTGTTAATGCCTATATTAACCTTGACCAGGGCTTTAACTGCAGAGTCACATGT +TGACACTGACTTAACAAAGCCTTACATTAAGTGGGATTTGTTAAAATATGACTTCACGGAAGAGAGGTTA +AAACTCTTTGACCGTTATTTTAAATATTGGGATCAGACATACCACCCAAATTGTGTTAACTGTTTGGATG +ACAGATGCATTCTGCATTGTGCAAACTTTAATGTTTTATTCTCTACAGTGTTCCCACCTACAAGTTTTGG +ACCACTAGTGAGAAAAATATTTGTTGATGGTGTTCCATTTGTAGTTTCAACTGGATACCACTTCAGAGAG +CTAGGTGTTGTACATAATCAGGATGTAAACTTACATAGCTCTAGACTTAGTTTTAAGGAATTACTTGTGT +ATGCTGCTGACCCTGCTATGCACGCTGCTTCTGGTAATCTATTACTAGATAAACGCACTACGTGCTTTTC +AGTAGCTGCACTTACTAACAATGTTGCTTTTCAAACTGTCAAACCCGGTAATTTTAACAAAGACTTCTAT +GACTTTGCTGTGTCTAAGGGTTTCTTTAAGGAAGGAAGTTCTGTTGAATTAAAACACTTCTTCTTTGCTC +AGGATGGTAATGCTGCTATCAGCGATTATGACTACTATCGTTATAATCTACCAACAATGTGTGATATCAG +ACAACTACTATTTGTAGTTGAAGTTGTTGATAAGTACTTTGATTGTTACGATGGTGGCTGTATTAATGCT +AACCAAGTCATCGTCAACAACCTAGACAAATCAGCTGGTTTTCCATTTAATAAATGGGGTAAGGCTAGAC +TTTATTATGATTCAATGAGTTATGAGGATCAAGATGCACTTTTCGCATATACAAAACGTAATGTCATCCC +TACTATAACTCAAATGAATCTTAAGTATGCCATTAGTGCAAAGAATAGAGCTCGCACCGTAGCTGGTGTC +TCTATCTGTAGTACTATGACCAATAGACAGTTTCATCAAAAATTATTGAAATCAATAGCCGCCACTAGAG +GAGCTACTGTAGTAATTGGAACAAGCAAATTCTATGGTGGTTGGCACAACATGTTAAAAACTGTTTATAG +TGATGTAGAAAACCCTCACCTTATGGGTTGGGATTATCCTAAATGTGATAGAGCCATGCCTAACATGCTT +AGAATTATGGCCTCACTTGTTCTTGCTCGCAAACATACAACGTGTTGTAGCTTGTCACACCGTTTCTATA +GATTAGCTAATGAGTGTGCTCAAGTATTGAGTGAAATGGTCATGTGTGGCGGTTCACTATATGTTAAACC +AGGTGGAACCTCATCAGGAGATGCCACAACTGCTTATGCTAATAGTGTTTTTAACATTTGTCAAGCTGTC +ACGGCCAATGTTAATGCACTTTTATCTACTGATGGTAACAAAATTGCCGATAAGTATGTCCGCAATTTAC +AACACAGACTTTATGAGTGTCTCTATAGAAATAGAGATGTTGACACAGACTTTGTGAATGAGTTTTACGC +ATATTTGCGTAAACATTTCTCAATGATGATACTCTCTGACGATGCTGTTGTGTGTTTCAATAGCACTTAT +GCATCTCAAGGTCTAGTGGCTAGCATAAAGAACTTTAAGTCAGTTCTTTATTATCAAAACAATGTTTTTA +TGTCTGAAGCAAAATGTTGGACTGAGACTGACCTTACTAAAGGACCTCATGAATTTTGCTCTCAACATAC +AATGCTAGTTAAACAGGGTGATGATTATGTGTACCTTCCTTACCCAGATCCATCAAGAATCCTAGGGGCC +GGCTGTTTTGTAGATGATATCGTAAAAACAGATGGTACACTTATGATTGAACGGTTCGTGTCTTTAGCTA +TAGATGCTTACCCACTTACTAAACATCCTAATCAGGAGTATGCTGATGTCTTTCATTTGTACTTACAATA +CATAAGAAAGCTACATGATGAGTTAACAGGACACATGTTAGACATGTATTCTGTTATGCTTACTAATGAT +AACACTTCAAGGTATTGGGAACCTGAGTTTTATGAGGCTATGTACACACCGCATACAGTCTTACAGGCTG +TTGGGGCTTGTGTTCTTTGCAATTCACAGACTTCATTAAGATGTGGTGCTTGCATACGTAGACCATTCTT +ATGTTGTAAATGCTGTTACGACCATGTCATATCAACATCACATAAATTAGTCTTGTCTGTTAATCCGTAT +GTTTGCAATGCTCCAGGTTGTGATGTCACAGATGTGACTCAACTTTACTTAGGAGGTATGAGCTATTATT +GTAAATCACATAAACCACCCATTAGTTTTCCATTGTGTGCTAATGGACAAGTTTTTGGTTTATATAAAAA +TACATGTGTTGGTAGCGATAATGTTACTGACTTTAATGCAATTGCAACATGTGACTGGACAAATGCTGGT +GATTACATTTTAGCTAACACCTGTACTGAAAGACTCAAGCTTTTTGCAGCAGAAACGCTCAAAGCTACTG +AGGAGACATTTAAACTGTCTTATGGTATTGCTACTGTACGTGAAGTGCTGTCTGACAGAGAATTACATCT +TTCATGGGAAGTTGGTAAACCTAGACCACCACTTAACCGAAATTATGTCTTTACTGGTTATCGTGTAACT +AAAAACAGTAAAGTACAAATAGGAGAGTACACCTTTGAAAAAGGTGACTATGGTGATGCTGTTGTTTACC +GAGGTACAACAACTTACAAATTAAATGTTGGTGATTATTTTGTGCTGACATCACATACAGTAATGCCATT +AAGTGCACCTACACTAGTGCCACAAGAGCACTATGTTAGAATTACTGGCTTATACCCAACACTCAATATC +TCAGATGAGTTTTCTAGCAATGTTGCAAATTATCAAAAGGTTGGTATGCAAAAGTATTCTACACTCCAGG +GACCACCTGGTACTGGTAAGAGTCATTTTGCTATTGGCCTAGCTCTCTACTACCCTTCTGCTCGCATAGT +GTATACAGCTTGCTCTCATGCCGCTGTTGATGCACTATGTGAGAAGGCATTAAAATATTTGCCTATAGAT +AAATGTAGTAGAATTATACCTGCACGTGCTCGTGTAGAGTGTTTTGATAAATTCAAAGTGAATTCAACAT +TAGAACAGTATGTCTTTTGTACTGTAAATGCATTGCCTGAGACGACAGCAGATATAGTTGTCTTTGATGA +AATTTCAATGGCCACAAATTATGATTTGAGTGTTGTCAATGCCAGATTACGTGCTAAGCACTATGTGTAC +ATTGGCGACCCTGCTCAATTACCTGCACCACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATT +TCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCC +TGCTGAAATTGTTGACACTGTGAGTGCTTTGGTTTATGATAATAAGCTTAAAGCACATAAAGACAAATCA +GCTCAATGCTTTAAAATGTTTTATAAGGGTGTTATCACGCATGATGTTTCATCTGCAATTAACAGGCCAC +AAATAGGCGTGGTAAGAGAATTCCTTACACGTAACCCTGCTTGGAGAAAAGCTGTCTTTATTTCACCTTA +TAATTCACAGAATGCTGTAGCCTCAAAGATTTTGGGACTACCAACTCAAACTGTTGATTCATCACAGGGC +TCAGAATATGACTATGTCATATTCACTCAAACCACTGAAACAGCTCACTCTTGTAATGTAAACAGATTTA +ATGTTGCTATTACCAGAGCAAAAGTAGGCATACTTTGCATAATGTCTGATAGAGACCTTTATGACAAGTT +GCAATTTACAAGTCTTGAAATTCCACGTAGGAATGTGGCAACTTTACAAGCTGAAAATGTAACAGGACTC +TTTAAAGATTGTAGTAAGGTAATCACTGGGTTACATCCTACACAGGCACCTACACACCTCAGTGTTGACA +CTAAATTCAAAACTGAAGGTTTATGTGTTGACATACCTGGCATACCTAAGGACATGACCTATAGAAGACT +CATCTCTATGATGGGTTTTAAAATGAATTATCAAGTTAATGGTTACCCTAACATGTTTATCACCCGCGAA +GAAGCTATAAGACATGTACGTGCATGGATTGGCTTCGATGTCGAGGGGTGTCATGCTACTAGAGAAGCTG +TTGGTACCAATTTACCTTTACAGCTAGGTTTTTCTACAGGTGTTAACCTAGTTGCTGTACCTACAGGTTA +TGTTGATACACCTAATAATACAGATTTTTCCAGAGTTAGTGCTAAACCACCGCCTGGAGATCAATTTAAA +CACCTCATACCACTTATGTACAAAGGACTTCCTTGGAATGTAGTGCGTATAAAGATTGTACAAATGTTAA +GTGACACACTTAAAAATCTCTCTGACAGAGTCGTATTTGTCTTATGGGCACATGGCTTTGAGTTGACATC +TATGAAGTATTTTGTGAAAATAGGACCTGAGCGCACCTGTTGTCTATGTGATAGACGTGCCACATGCTTT +TCCACTGCTTCAGACACTTATGCCTGTTGGCATCATTCTATTGGATTTGATTACGTCTATAATCCGTTTA +TGATTGATGTTCAACAATGGGGTTTTACAGGTAACCTACAAAGCAACCATGATCTGTATTGTCAAGTCCA +TGGTAATGCACATGTAGCTAGTTGTGATGCAATCATGACTAGGTGTCTAGCTGTCCACGAGTGCTTTGTT +AAGCGTGTTGACTGGACTATTGAATATCCTATAATTGGTGATGAACTGAAGATTAATGCGGCTTGTAGAA +AGGTTCAACACATGGTTGTTAAAGCTGCATTATTAGCAGACAAATTCCCAGTTCTTCACGACATTGGTAA +CCCTAAAGCTATTAAGTGTGTACCTCAAGCTGATGTAGAATGGAAGTTCTATGATGCACAGCCTTGTAGT +GACAAAGCTTATAAAATAGAAGAATTATTCTATTCTTATGCCACACATTCTGACAAATTCACAGATGGTG +TATGCCTATTTTGGAATTGCAATGTCGATAGATATCCTGCTAATTCCATTGTTTGTAGATTTGACACTAG +AGTGCTATCTAACCTTAACTTGCCTGGTTGTGATGGTGGCAGTTTGTATGTAAATAAACATGCATTCCAC +ACACCAGCTTTTGATAAAAGTGCTTTTGTTAATTTAAAACAATTACCATTTTTCTATTACTCTGACAGTC +CATGTGAGTCTCATGGAAAACAAGTAGTGTCAGATATAGATTATGTACCACTAAAGTCTGCTACGTGTAT +AACACGTTGCAATTTAGGTGGTGCTGTCTGTAGACATCATGCTAATGAGTACAGATTGTATCTCGATGCT +TATAACATGATGATCTCAGCTGGCTTTAGCTTGTGGGTTTACAAACAATTTGATACTTATAACCTCTGGA +ACACTTTTACAAGACTTCAGAGTTTAGAAAATGTGGCTTTTAATGTTGTAAATAAGGGACACTTTGATGG +ACAACAGGGTGAAGTACCAGTTTCTATCATTAATAACACTGTTTACACAAAAGTTGATGGTGTTGATGTA +GAATTGTTTGAAAATAAAACAACATTACCTGTTAATGTAGCATTTGAGCTTTGGGCTAAGCGCAACATTA +AACCAGTACCAGAGGTGAAAATACTCAATAATTTGGGTGTGGACATTGCTGCTAATACTGTGATCTGGGA +CTACAAAAGAGATGCTCCAGCACATATATCTACTATTGGTGTTTGTTCTATGACTGACATAGCCAAGAAA +CCAACTGAAACGATTTGTGCACCACTCACTGTCTTTTTTGATGGTAGAGTTGATGGTCAAGTAGACTTAT +TTAGAAATGCCCGTAATGGTGTTCTTATTACAGAAGGTAGTGTTAAAGGTTTACAACCATCTGTAGGTCC +CAAACAAGCTAGTCTTAATGGAGTCACATTAATTGGAGAAGCCGTAAAAACACAGTTCAATTATTATAAG +AAAGTTGATGGTGTTGTCCAACAATTACCTGAAACTTACTTTACTCAGAGTAGAAATTTACAAGAATTTA +AACCCAGGAGTCAAATGGAAATTGATTTCTTAGAATTAGCTATGGATGAATTCATTGAACGGTATAAATT +AGAAGGCTATGCCTTCGAACATATCGTTTATGGAGATTTTAGTCATAGTCAGTTAGGTGGTTTACATCTA +CTGATTGGACTAGCTAAACGTTTTAAGGAATCACCTTTTGAATTAGAAGATTTTATTCCTATGGACAGTA +CAGTTAAAAACTATTTCATAACAGATGCGCAAACAGGTTCATCTAAGTGTGTGTGTTCTGTTATTGATTT +ATTACTTGATGATTTTGTTGAAATAATAAAATCCCAAGATTTATCTGTAGTTTCTAAGGTTGTCAAAGTG +ACTATTGACTATACAGAAATTTCATTTATGCTTTGGTGTAAAGATGGCCATGTAGAAACATTTTACCCAA +AATTACAATCTAGTCAAGCGTGGCAACCGGGTGTTGCTATGCCTAATCTTTACAAAATGCAAAGAATGCT +ATTAGAAAAGTGTGACCTTCAAAATTATGGTGATAGTGCAACATTACCTAAAGGCATAATGATGAATGTC +GCAAAATATACTCAACTGTGTCAATATTTAAACACATTAACATTAGCTGTACCCTATAATATGAGAGTTA +TACATTTTGGTGCTGGTTCTGATAAAGGAGTTGCACCAGGTACAGCTGTTTTAAGACAGTGGTTGCCTAC +GGGTACGCTGCTTGTCGATTCAGATCTTAATGACTTTGTCTCTGATGCAGATTCAACTTTGATTGGTGAT +TGTGCAACTGTACATACAGCTAATAAATGGGATCTCATTATTAGTGATATGTACGACCCTAAGACTAAAA +ATGTTACAAAAGAAAATGACTCTAAAGAGGGTTTTTTCACTTACATTTGTGGGTTTATACAACAAAAGCT +AGCTCTTGGAGGTTCCGTGGCTATAAAGATAACAGAACATTCTTGGAATGCTGATCTTTATAAGCTCATG +GGACACTTCGCATGGTGGACAGCCTTTGTTACTAATGTGAATGCGTCATCATCTGAAGCATTTTTAATTG +GATGTAATTATCTTGGCAAACCACGCGAACAAATAGATGGTTATGTCATGCATGCAAATTACATATTTTG +GAGGAATACAAATCCAATTCAGTTGTCTTCCTATTCTTTATTTGACATGAGTAAATTTCCCCTTAAATTA +AGGGGTACTGCTGTTATGTCTTTAAAAGAAGGTCAAATCAATGATATGATTTTATCTCTTCTTAGTAAAG +GTAGACTTATAATTAGAGAAAACAACAGAGTTGTTATTTCTAGTGATGTTCTTGTTAACAACTAAACGAA +CAATGTTTGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACCAGAACTCA +ATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGACAAAGTTTTCAGATCCTCA +GTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCCAATGTTACTTGGTTCCATGCTATACATG +TCTCTGGGACCAATGGTACTAAGAGGTTTGATAACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGC +TTCCACTGAGAAGTCTAACATAATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCC +CTACTTATTGTTAATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATGATCCAT +TTTTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTATTCTAGTGC +GAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAAGGAAAACAGGGTAATTTC +AAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTATTTTAAAATATATTCTAAGCACACGCCTA +TTAATTTAGTGCGTGATCTCCCTCAGGGTTTTTCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTAT +TAACATCACTAGGTTTCAAACTTTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCA +GGTTGGACAGCTGGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATA +ATGAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAGTGTACGTT +GAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTCCAACCAACAGAATCTATT +GTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAAGTTTTTAACGCCACCAGATTTGCATCTG +TTTATGCTTGGAACAGGAAGAGAATCAGCAACTGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATC +ATTTTCCACTTTTAAGTGTTATGGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTAT +GCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTG +ATTATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAATCTTGATTC +TAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAATCTCAAACCTTTTGAGAGA 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-MN908947.3 20677 20699 SARS-CoV-2_69_LEFT 1 -MN908947.3 20766 20792 SARS-CoV-2_68_RIGHT 2 -MN908947.3 20988 21013 SARS-CoV-2_70_LEFT 2 -MN908947.3 21050 21080 SARS-CoV-2_69_RIGHT 1 -MN908947.3 21294 21316 SARS-CoV-2_71_LEFT 1 -MN908947.3 21358 21387 SARS-CoV-2_70_RIGHT 2 -MN908947.3 21532 21561 SARS-CoV-2_72_LEFT 2 -MN908947.3 21675 21700 SARS-CoV-2_71_RIGHT 1 -MN908947.3 21865 21889 SARS-CoV-2_73_LEFT 1 -MN908947.3 21904 21933 SARS-CoV-2_72_RIGHT 2 -MN908947.3 22091 22113 SARS-CoV-2_74_LEFT 2 -MN908947.3 22247 22274 SARS-CoV-2_73_RIGHT 1 -MN908947.3 22402 22428 SARS-CoV-2_75_LEFT 1 -MN908947.3 22474 22503 SARS-CoV-2_74_RIGHT 2 -MN908947.3 22648 22677 SARS-CoV-2_76_LEFT 2 -MN908947.3 22742 22774 SARS-CoV-2_76_LEFT_alt1 2 -MN908947.3 22785 22805 SARS-CoV-2_75_RIGHT 1 -MN908947.3 22944 22974 SARS-CoV-2_77_LEFT 1 -MN908947.3 23028 23057 SARS-CoV-2_76_RIGHT 2 -MN908947.3 23120 23141 SARS-CoV-2_76_RIGHT_alt1 2 -MN908947.3 23219 23246 SARS-CoV-2_78_LEFT 2 -MN908947.3 23327 23351 SARS-CoV-2_77_RIGHT 1 -MN908947.3 23553 23575 SARS-CoV-2_79_LEFT 1 -MN908947.3 23611 23635 SARS-CoV-2_78_RIGHT 2 -MN908947.3 23853 23876 SARS-CoV-2_80_LEFT 2 -MN908947.3 23914 23944 SARS-CoV-2_79_RIGHT_alt1 1 -MN908947.3 23927 23955 SARS-CoV-2_79_RIGHT 1 -MN908947.3 24171 24194 SARS-CoV-2_81_LEFT 1 -MN908947.3 24233 24258 SARS-CoV-2_80_RIGHT 2 -MN908947.3 24426 24448 SARS-CoV-2_82_LEFT 2 -MN908947.3 24545 24567 SARS-CoV-2_81_RIGHT 1 -MN908947.3 24750 24772 SARS-CoV-2_83_LEFT 1 -MN908947.3 24814 24836 SARS-CoV-2_82_RIGHT 2 -MN908947.3 25051 25076 SARS-CoV-2_84_LEFT 2 -MN908947.3 25122 25150 SARS-CoV-2_83_RIGHT 1 -MN908947.3 25331 25353 SARS-CoV-2_85_LEFT 1 -MN908947.3 25438 25461 SARS-CoV-2_84_RIGHT 2 -MN908947.3 25645 25672 SARS-CoV-2_86_LEFT 2 -MN908947.3 25711 25740 SARS-CoV-2_85_RIGHT 1 -MN908947.3 25951 25979 SARS-CoV-2_87_LEFT 1 -MN908947.3 26026 26050 SARS-CoV-2_86_RIGHT 2 -MN908947.3 26242 26268 SARS-CoV-2_88_LEFT_alt1 2 -MN908947.3 26255 26277 SARS-CoV-2_88_LEFT 2 -MN908947.3 26338 26360 SARS-CoV-2_87_RIGHT 1 -MN908947.3 26564 26587 SARS-CoV-2_89_LEFT 1 -MN908947.3 26592 26621 SARS-CoV-2_89_LEFT_alt1 1 -MN908947.3 26635 26661 SARS-CoV-2_88_RIGHT 2 -MN908947.3 26873 26895 SARS-CoV-2_90_LEFT 2 -MN908947.3 26956 26979 SARS-CoV-2_89_RIGHT 1 -MN908947.3 26966 26991 SARS-CoV-2_89_RIGHT_alt1 1 -MN908947.3 27152 27177 SARS-CoV-2_91_LEFT 1 -MN908947.3 27218 27251 SARS-CoV-2_90_RIGHT_alt1 2 -MN908947.3 27256 27283 SARS-CoV-2_90_RIGHT 2 -MN908947.3 27447 27473 SARS-CoV-2_92_LEFT 2 -MN908947.3 27534 27560 SARS-CoV-2_91_RIGHT 1 -MN908947.3 27700 27726 SARS-CoV-2_93_LEFT 1 -MN908947.3 27826 27855 SARS-CoV-2_92_RIGHT 2 -MN908947.3 27996 28021 SARS-CoV-2_94_LEFT 2 -MN908947.3 28082 28104 SARS-CoV-2_93_RIGHT 1 -MN908947.3 28190 28214 SARS-CoV-2_95_LEFT 1 -MN908947.3 28394 28416 SARS-CoV-2_94_RIGHT 2 -MN908947.3 28512 28536 SARS-CoV-2_96_LEFT 2 -MN908947.3 28572 28598 SARS-CoV-2_95_RIGHT 1 -MN908947.3 28827 28849 SARS-CoV-2_97_LEFT 1 -MN908947.3 28893 28914 SARS-CoV-2_96_RIGHT 2 -MN908947.3 29136 29161 SARS-CoV-2_98_LEFT 2 -MN908947.3 29206 29227 SARS-CoV-2_97_RIGHT 1 -MN908947.3 29452 29475 SARS-CoV-2_99_LEFT 1 -MN908947.3 29512 29534 SARS-CoV-2_98_RIGHT 2 -MN908947.3 29827 29854 SARS-CoV-2_99_RIGHT 1 diff --git a/test/data/broken/info-yml/extra-field/info.yml b/test/data/broken/info-yml/extra-field/info.yml new file mode 100644 index 0000000..63db3ce --- /dev/null +++ b/test/data/broken/info-yml/extra-field/info.yml @@ -0,0 +1,23 @@ +favourite_mountain: eiger +schema_version: 1.0.0-alpha +name: artic +amplicon_size: 400 +version: v4.1 +organism: sars-cov-2 +aliases: +- ARTIC/V4.1 +developers: +- ARTIC network +vendors: +- organisation_name: IDT + kit_name: '10011442' +- organisation_name: Eurofins + home_page: https://eurofinsgenomics.com +definition_url: https://github.com/pha4ge/primer-schemes/tree/main/sars-cov-2/artic/v4.1 +source_url: https://github.com/quick-lab/primerschemes/tree/main/primerschemes/artic-sars-cov-2/400/v4.1.0 +citations: +- https://doi.org/10.1101%2F2020.09.04.283077 +derived_from: artic-v4 +license: CC-BY-SA-4.0 +primer_checksum: primaschema:8eaf6a2fb31f602a +reference_checksum: primaschema:b1acd7163146bf17 diff --git a/test/data/broken/info-yml/extra-field/primer.bed b/test/data/broken/info-yml/extra-field/primer.bed new file mode 100644 index 0000000..3279bff --- /dev/null +++ b/test/data/broken/info-yml/extra-field/primer.bed @@ -0,0 +1,4 @@ +MN908947.3 25 50 SARS-CoV-2_1_LEFT_1 1 + AACAAACCAACCAACTTTCGATCTC +MN908947.3 408 431 SARS-CoV-2_1_RIGHT_1 1 - CTTCTACTAAGCCACAAGTGCCA +MN908947.3 324 344 SARS-CoV-2_2_LEFT_1 2 + TTTACAGGTTCGCGACGTGC +MN908947.3 705 727 SARS-CoV-2_2_RIGHT_1 2 - ATAAGGATCAGTGCCAAGCTCG \ No newline at end of file diff --git a/test/data/broken/info-yml/extra-field/reference.fasta b/test/data/broken/info-yml/extra-field/reference.fasta new file mode 100644 index 0000000..e1cfd92 --- /dev/null +++ b/test/data/broken/info-yml/extra-field/reference.fasta @@ -0,0 +1,429 @@ +>MN908947.3 +ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAA +CGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAAC +TAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTG +TTGCAGCCGATCATCAGCACATCTAGGTTTCGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTC +CCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTAC +GTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGG +CTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAAACGTTCGGAT +GCTCGAACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACTCGAAGGCATTCAGTACGGTC +GTAGTGGTGAGACACTTGGTGTCCTTGTCCCTCATGTGGGCGAAATACCAGTGGCTTACCGCAAGGTTCT +TCTTCGTAAGAACGGTAATAAAGGAGCTGGTGGCCATAGTTACGGCGCCGATCTAAAGTCATTTGACTTA +GGCGACGAGCTTGGCACTGATCCTTATGAAGATTTTCAAGAAAACTGGAACACTAAACATAGCAGTGGTG +TTACCCGTGAACTCATGCGTGAGCTTAACGGAGGGGCATACACTCGCTATGTCGATAACAACTTCTGTGG +CCCTGATGGCTACCCTCTTGAGTGCATTAAAGACCTTCTAGCACGTGCTGGTAAAGCTTCATGCACTTTG +TCCGAACAACTGGACTTTATTGACACTAAGAGGGGTGTATACTGCTGCCGTGAACATGAGCATGAAATTG +CTTGGTACACGGAACGTTCTGAAAAGAGCTATGAATTGCAGACACCTTTTGAAATTAAATTGGCAAAGAA +ATTTGACACCTTCAATGGGGAATGTCCAAATTTTGTATTTCCCTTAAATTCCATAATCAAGACTATTCAA +CCAAGGGTTGAAAAGAAAAAGCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCCAGTTGCGTCAC +CAAATGAATGCAACCAAATGTGCCTTTCAACTCTCATGAAGTGTGATCATTGTGGTGAAACTTCATGGCA +GACGGGCGATTTTGTTAAAGCCACTTGCGAATTTTGTGGCACTGAGAATTTGACTAAAGAAGGTGCCACT +ACTTGTGGTTACTTACCCCAAAATGCTGTTGTTAAAATTTATTGTCCAGCATGTCACAATTCAGAAGTAG +GACCTGAGCATAGTCTTGCCGAATACCATAATGAATCTGGCTTGAAAACCATTCTTCGTAAGGGTGGTCG +CACTATTGCCTTTGGAGGCTGTGTGTTCTCTTATGTTGGTTGCCATAACAAGTGTGCCTATTGGGTTCCA +CGTGCTAGCGCTAACATAGGTTGTAACCATACAGGTGTTGTTGGAGAAGGTTCCGAAGGTCTTAATGACA +ACCTTCTTGAAATACTCCAAAAAGAGAAAGTCAACATCAATATTGTTGGTGACTTTAAACTTAATGAAGA +GATCGCCATTATTTTGGCATCTTTTTCTGCTTCCACAAGTGCTTTTGTGGAAACTGTGAAAGGTTTGGAT +TATAAAGCATTCAAACAAATTGTTGAATCCTGTGGTAATTTTAAAGTTACAAAAGGAAAAGCTAAAAAAG +GTGCCTGGAATATTGGTGAACAGAAATCAATACTGAGTCCTCTTTATGCATTTGCATCAGAGGCTGCTCG +TGTTGTACGATCAATTTTCTCCCGCACTCTTGAAACTGCTCAAAATTCTGTGCGTGTTTTACAGAAGGCC +GCTATAACAATACTAGATGGAATTTCACAGTATTCACTGAGACTCATTGATGCTATGATGTTCACATCTG +ATTTGGCTACTAACAATCTAGTTGTAATGGCCTACATTACAGGTGGTGTTGTTCAGTTGACTTCGCAGTG +GCTAACTAACATCTTTGGCACTGTTTATGAAAAACTCAAACCCGTCCTTGATTGGCTTGAAGAGAAGTTT +AAGGAAGGTGTAGAGTTTCTTAGAGACGGTTGGGAAATTGTTAAATTTATCTCAACCTGTGCTTGTGAAA +TTGTCGGTGGACAAATTGTCACCTGTGCAAAGGAAATTAAGGAGAGTGTTCAGACATTCTTTAAGCTTGT +AAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGCCTTGAATTTA +GGTGAAACATTTGTCACGCACTCAAAGGGATTGTACAGAAAGTGTGTTAAATCCAGAGAAGAAACTGGCC +TACTCATGCCTCTAAAAGCCCCAAAAGAAATTATCTTCTTAGAGGGAGAAACACTTCCCACAGAAGTGTT +AACAGAGGAAGTTGTCTTGAAAACTGGTGATTTACAACCATTAGAACAACCTACTAGTGAAGCTGTTGAA +GCTCCATTGGTTGGTACACCAGTTTGTATTAACGGGCTTATGTTGCTCGAAATCAAAGACACAGAAAAGT +ACTGTGCCCTTGCACCTAATATGATGGTAACAAACAATACCTTCACACTCAAAGGCGGTGCACCAACAAA +GGTTACTTTTGGTGATGACACTGTGATAGAAGTGCAAGGTTACAAGAGTGTGAATATCACTTTTGAACTT +GATGAAAGGATTGATAAAGTACTTAATGAGAAGTGCTCTGCCTATACAGTTGAACTCGGTACAGAAGTAA +ATGAGTTCGCCTGTGTTGTGGCAGATGCTGTCATAAAAACTTTGCAACCAGTATCTGAATTACTTACACC +ACTGGGCATTGATTTAGATGAGTGGAGTATGGCTACATACTACTTATTTGATGAGTCTGGTGAGTTTAAA +TTGGCTTCACATATGTATTGTTCTTTCTACCCTCCAGATGAGGATGAAGAAGAAGGTGATTGTGAAGAAG +AAGAGTTTGAGCCATCAACTCAATATGAGTATGGTACTGAAGATGATTACCAAGGTAAACCTTTGGAATT +TGGTGCCACTTCTGCTGCTCTTCAACCTGAAGAAGAGCAAGAAGAAGATTGGTTAGATGATGATAGTCAA +CAAACTGTTGGTCAACAAGACGGCAGTGAGGACAATCAGACAACTACTATTCAAACAATTGTTGAGGTTC +AACCTCAATTAGAGATGGAACTTACACCAGTTGTTCAGACTATTGAAGTGAATAGTTTTAGTGGTTATTT +AAAACTTACTGACAATGTATACATTAAAAATGCAGACATTGTGGAAGAAGCTAAAAAGGTAAAACCAACA +GTGGTTGTTAATGCAGCCAATGTTTACCTTAAACATGGAGGAGGTGTTGCAGGAGCCTTAAATAAGGCTA +CTAACAATGCCATGCAAGTTGAATCTGATGATTACATAGCTACTAATGGACCACTTAAAGTGGGTGGTAG +TTGTGTTTTAAGCGGACACAATCTTGCTAAACACTGTCTTCATGTTGTCGGCCCAAATGTTAACAAAGGT +GAAGACATTCAACTTCTTAAGAGTGCTTATGAAAATTTTAATCAGCACGAAGTTCTACTTGCACCATTAT +TATCAGCTGGTATTTTTGGTGCTGACCCTATACATTCTTTAAGAGTTTGTGTAGATACTGTTCGCACAAA +TGTCTACTTAGCTGTCTTTGATAAAAATCTCTATGACAAACTTGTTTCAAGCTTTTTGGAAATGAAGAGT +GAAAAGCAAGTTGAACAAAAGATCGCTGAGATTCCTAAAGAGGAAGTTAAGCCATTTATAACTGAAAGTA +AACCTTCAGTTGAACAGAGAAAACAAGATGATAAGAAAATCAAAGCTTGTGTTGAAGAAGTTACAACAAC +TCTGGAAGAAACTAAGTTCCTCACAGAAAACTTGTTACTTTATATTGACATTAATGGCAATCTTCATCCA +GATTCTGCCACTCTTGTTAGTGACATTGACATCACTTTCTTAAAGAAAGATGCTCCATATATAGTGGGTG +ATGTTGTTCAAGAGGGTGTTTTAACTGCTGTGGTTATACCTACTAAAAAGGCTGGTGGCACTACTGAAAT +GCTAGCGAAAGCTTTGAGAAAAGTGCCAACAGACAATTATATAACCACTTACCCGGGTCAGGGTTTAAAT +GGTTACACTGTAGAGGAGGCAAAGACAGTGCTTAAAAAGTGTAAAAGTGCCTTTTACATTCTACCATCTA +TTATCTCTAATGAGAAGCAAGAAATTCTTGGAACTGTTTCTTGGAATTTGCGAGAAATGCTTGCACATGC +AGAAGAAACACGCAAATTAATGCCTGTCTGTGTGGAAACTAAAGCCATAGTTTCAACTATACAGCGTAAA +TATAAGGGTATTAAAATACAAGAGGGTGTGGTTGATTATGGTGCTAGATTTTACTTTTACACCAGTAAAA +CAACTGTAGCGTCACTTATCAACACACTTAACGATCTAAATGAAACTCTTGTTACAATGCCACTTGGCTA +TGTAACACATGGCTTAAATTTGGAAGAAGCTGCTCGGTATATGAGATCTCTCAAAGTGCCAGCTACAGTT +TCTGTTTCTTCACCTGATGCTGTTACAGCGTATAATGGTTATCTTACTTCTTCTTCTAAAACACCTGAAG +AACATTTTATTGAAACCATCTCACTTGCTGGTTCCTATAAAGATTGGTCCTATTCTGGACAATCTACACA +ACTAGGTATAGAATTTCTTAAGAGAGGTGATAAAAGTGTATATTACACTAGTAATCCTACCACATTCCAC +CTAGATGGTGAAGTTATCACCTTTGACAATCTTAAGACACTTCTTTCTTTGAGAGAAGTGAGGACTATTA +AGGTGTTTACAACAGTAGACAACATTAACCTCCACACGCAAGTTGTGGACATGTCAATGACATATGGACA +ACAGTTTGGTCCAACTTATTTGGATGGAGCTGATGTTACTAAAATAAAACCTCATAATTCACATGAAGGT +AAAACATTTTATGTTTTACCTAATGATGACACTCTACGTGTTGAGGCTTTTGAGTACTACCACACAACTG +ATCCTAGTTTTCTGGGTAGGTACATGTCAGCATTAAATCACACTAAAAAGTGGAAATACCCACAAGTTAA +TGGTTTAACTTCTATTAAATGGGCAGATAACAACTGTTATCTTGCCACTGCATTGTTAACACTCCAACAA +ATAGAGTTGAAGTTTAATCCACCTGCTCTACAAGATGCTTATTACAGAGCAAGGGCTGGTGAAGCTGCTA +ACTTTTGTGCACTTATCTTAGCCTACTGTAATAAGACAGTAGGTGAGTTAGGTGATGTTAGAGAAACAAT +GAGTTACTTGTTTCAACATGCCAATTTAGATTCTTGCAAAAGAGTCTTGAACGTGGTGTGTAAAACTTGT +GGACAACAGCAGACAACCCTTAAGGGTGTAGAAGCTGTTATGTACATGGGCACACTTTCTTATGAACAAT +TTAAGAAAGGTGTTCAGATACCTTGTACGTGTGGTAAACAAGCTACAAAATATCTAGTACAACAGGAGTC +ACCTTTTGTTATGATGTCAGCACCACCTGCTCAGTATGAACTTAAGCATGGTACATTTACTTGTGCTAGT +GAGTACACTGGTAATTACCAGTGTGGTCACTATAAACATATAACTTCTAAAGAAACTTTGTATTGCATAG +ACGGTGCTTTACTTACAAAGTCCTCAGAATACAAAGGTCCTATTACGGATGTTTTCTACAAAGAAAACAG +TTACACAACAACCATAAAACCAGTTACTTATAAATTGGATGGTGTTGTTTGTACAGAAATTGACCCTAAG +TTGGACAATTATTATAAGAAAGACAATTCTTATTTCACAGAGCAACCAATTGATCTTGTACCAAACCAAC +CATATCCAAACGCAAGCTTCGATAATTTTAAGTTTGTATGTGATAATATCAAATTTGCTGATGATTTAAA +CCAGTTAACTGGTTATAAGAAACCTGCTTCAAGAGAGCTTAAAGTTACATTTTTCCCTGACTTAAATGGT +GATGTGGTGGCTATTGATTATAAACACTACACACCCTCTTTTAAGAAAGGAGCTAAATTGTTACATAAAC +CTATTGTTTGGCATGTTAACAATGCAACTAATAAAGCCACGTATAAACCAAATACCTGGTGTATACGTTG +TCTTTGGAGCACAAAACCAGTTGAAACATCAAATTCGTTTGATGTACTGAAGTCAGAGGACGCGCAGGGA +ATGGATAATCTTGCCTGCGAAGATCTAAAACCAGTCTCTGAAGAAGTAGTGGAAAATCCTACCATACAGA +AAGACGTTCTTGAGTGTAATGTGAAAACTACCGAAGTTGTAGGAGACATTATACTTAAACCAGCAAATAA +TAGTTTAAAAATTACAGAAGAGGTTGGCCACACAGATCTAATGGCTGCTTATGTAGACAATTCTAGTCTT +ACTATTAAGAAACCTAATGAATTATCTAGAGTATTAGGTTTGAAAACCCTTGCTACTCATGGTTTAGCTG +CTGTTAATAGTGTCCCTTGGGATACTATAGCTAATTATGCTAAGCCTTTTCTTAACAAAGTTGTTAGTAC +AACTACTAACATAGTTACACGGTGTTTAAACCGTGTTTGTACTAATTATATGCCTTATTTCTTTACTTTA +TTGCTACAATTGTGTACTTTTACTAGAAGTACAAATTCTAGAATTAAAGCATCTATGCCGACTACTATAG +CAAAGAATACTGTTAAGAGTGTCGGTAAATTTTGTCTAGAGGCTTCATTTAATTATTTGAAGTCACCTAA +TTTTTCTAAACTGATAAATATTATAATTTGGTTTTTACTATTAAGTGTTTGCCTAGGTTCTTTAATCTAC +TCAACCGCTGCTTTAGGTGTTTTAATGTCTAATTTAGGCATGCCTTCTTACTGTACTGGTTACAGAGAAG +GCTATTTGAACTCTACTAATGTCACTATTGCAACCTACTGTACTGGTTCTATACCTTGTAGTGTTTGTCT +TAGTGGTTTAGATTCTTTAGACACCTATCCTTCTTTAGAAACTATACAAATTACCATTTCATCTTTTAAA +TGGGATTTAACTGCTTTTGGCTTAGTTGCAGAGTGGTTTTTGGCATATATTCTTTTCACTAGGTTTTTCT +ATGTACTTGGATTGGCTGCAATCATGCAATTGTTTTTCAGCTATTTTGCAGTACATTTTATTAGTAATTC +TTGGCTTATGTGGTTAATAATTAATCTTGTACAAATGGCCCCGATTTCAGCTATGGTTAGAATGTACATC +TTCTTTGCATCATTTTATTATGTATGGAAAAGTTATGTGCATGTTGTAGACGGTTGTAATTCATCAACTT +GTATGATGTGTTACAAACGTAATAGAGCAACAAGAGTCGAATGTACAACTATTGTTAATGGTGTTAGAAG +GTCCTTTTATGTCTATGCTAATGGAGGTAAAGGCTTTTGCAAACTACACAATTGGAATTGTGTTAATTGT +GATACATTCTGTGCTGGTAGTACATTTATTAGTGATGAAGTTGCGAGAGACTTGTCACTACAGTTTAAAA +GACCAATAAATCCTACTGACCAGTCTTCTTACATCGTTGATAGTGTTACAGTGAAGAATGGTTCCATCCA +TCTTTACTTTGATAAAGCTGGTCAAAAGACTTATGAAAGACATTCTCTCTCTCATTTTGTTAACTTAGAC +AACCTGAGAGCTAATAACACTAAAGGTTCATTGCCTATTAATGTTATAGTTTTTGATGGTAAATCAAAAT +GTGAAGAATCATCTGCAAAATCAGCGTCTGTTTACTACAGTCAGCTTATGTGTCAACCTATACTGTTACT +AGATCAGGCATTAGTGTCTGATGTTGGTGATAGTGCGGAAGTTGCAGTTAAAATGTTTGATGCTTACGTT +AATACGTTTTCATCAACTTTTAACGTACCAATGGAAAAACTCAAAACACTAGTTGCAACTGCAGAAGCTG +AACTTGCAAAGAATGTGTCCTTAGACAATGTCTTATCTACTTTTATTTCAGCAGCTCGGCAAGGGTTTGT +TGATTCAGATGTAGAAACTAAAGATGTTGTTGAATGTCTTAAATTGTCACATCAATCTGACATAGAAGTT +ACTGGCGATAGTTGTAATAACTATATGCTCACCTATAACAAAGTTGAAAACATGACACCCCGTGACCTTG +GTGCTTGTATTGACTGTAGTGCGCGTCATATTAATGCGCAGGTAGCAAAAAGTCACAACATTGCTTTGAT +ATGGAACGTTAAAGATTTCATGTCATTGTCTGAACAACTACGAAAACAAATACGTAGTGCTGCTAAAAAG +AATAACTTACCTTTTAAGTTGACATGTGCAACTACTAGACAAGTTGTTAATGTTGTAACAACAAAGATAG +CACTTAAGGGTGGTAAAATTGTTAATAATTGGTTGAAGCAGTTAATTAAAGTTACACTTGTGTTCCTTTT +TGTTGCTGCTATTTTCTATTTAATAACACCTGTTCATGTCATGTCTAAACATACTGACTTTTCAAGTGAA +ATCATAGGATACAAGGCTATTGATGGTGGTGTCACTCGTGACATAGCATCTACAGATACTTGTTTTGCTA +ACAAACATGCTGATTTTGACACATGGTTTAGCCAGCGTGGTGGTAGTTATACTAATGACAAAGCTTGCCC +ATTGATTGCTGCAGTCATAACAAGAGAAGTGGGTTTTGTCGTGCCTGGTTTGCCTGGCACGATATTACGC +ACAACTAATGGTGACTTTTTGCATTTCTTACCTAGAGTTTTTAGTGCAGTTGGTAACATCTGTTACACAC +CATCAAAACTTATAGAGTACACTGACTTTGCAACATCAGCTTGTGTTTTGGCTGCTGAATGTACAATTTT +TAAAGATGCTTCTGGTAAGCCAGTACCATATTGTTATGATACCAATGTACTAGAAGGTTCTGTTGCTTAT +GAAAGTTTACGCCCTGACACACGTTATGTGCTCATGGATGGCTCTATTATTCAATTTCCTAACACCTACC +TTGAAGGTTCTGTTAGAGTGGTAACAACTTTTGATTCTGAGTACTGTAGGCACGGCACTTGTGAAAGATC +AGAAGCTGGTGTTTGTGTATCTACTAGTGGTAGATGGGTACTTAACAATGATTATTACAGATCTTTACCA +GGAGTTTTCTGTGGTGTAGATGCTGTAAATTTACTTACTAATATGTTTACACCACTAATTCAACCTATTG +GTGCTTTGGACATATCAGCATCTATAGTAGCTGGTGGTATTGTAGCTATCGTAGTAACATGCCTTGCCTA +CTATTTTATGAGGTTTAGAAGAGCTTTTGGTGAATACAGTCATGTAGTTGCCTTTAATACTTTACTATTC +CTTATGTCATTCACTGTACTCTGTTTAACACCAGTTTACTCATTCTTACCTGGTGTTTATTCTGTTATTT +ACTTGTACTTGACATTTTATCTTACTAATGATGTTTCTTTTTTAGCACATATTCAGTGGATGGTTATGTT +CACACCTTTAGTACCTTTCTGGATAACAATTGCTTATATCATTTGTATTTCCACAAAGCATTTCTATTGG +TTCTTTAGTAATTACCTAAAGAGACGTGTAGTCTTTAATGGTGTTTCCTTTAGTACTTTTGAAGAAGCTG +CGCTGTGCACCTTTTTGTTAAATAAAGAAATGTATCTAAAGTTGCGTAGTGATGTGCTATTACCTCTTAC +GCAATATAATAGATACTTAGCTCTTTATAATAAGTACAAGTATTTTAGTGGAGCAATGGATACAACTAGC +TACAGAGAAGCTGCTTGTTGTCATCTCGCAAAGGCTCTCAATGACTTCAGTAACTCAGGTTCTGATGTTC +TTTACCAACCACCACAAACCTCTATCACCTCAGCTGTTTTGCAGAGTGGTTTTAGAAAAATGGCATTCCC +ATCTGGTAAAGTTGAGGGTTGTATGGTACAAGTAACTTGTGGTACAACTACACTTAACGGTCTTTGGCTT +GATGACGTAGTTTACTGTCCAAGACATGTGATCTGCACCTCTGAAGACATGCTTAACCCTAATTATGAAG +ATTTACTCATTCGTAAGTCTAATCATAATTTCTTGGTACAGGCTGGTAATGTTCAACTCAGGGTTATTGG +ACATTCTATGCAAAATTGTGTACTTAAGCTTAAGGTTGATACAGCCAATCCTAAGACACCTAAGTATAAG +TTTGTTCGCATTCAACCAGGACAGACTTTTTCAGTGTTAGCTTGTTACAATGGTTCACCATCTGGTGTTT +ACCAATGTGCTATGAGGCCCAATTTCACTATTAAGGGTTCATTCCTTAATGGTTCATGTGGTAGTGTTGG +TTTTAACATAGATTATGACTGTGTCTCTTTTTGTTACATGCACCATATGGAATTACCAACTGGAGTTCAT +GCTGGCACAGACTTAGAAGGTAACTTTTATGGACCTTTTGTTGACAGGCAAACAGCACAAGCAGCTGGTA +CGGACACAACTATTACAGTTAATGTTTTAGCTTGGTTGTACGCTGCTGTTATAAATGGAGACAGGTGGTT +TCTCAATCGATTTACCACAACTCTTAATGACTTTAACCTTGTGGCTATGAAGTACAATTATGAACCTCTA +ACACAAGACCATGTTGACATACTAGGACCTCTTTCTGCTCAAACTGGAATTGCCGTTTTAGATATGTGTG +CTTCATTAAAAGAATTACTGCAAAATGGTATGAATGGACGTACCATATTGGGTAGTGCTTTATTAGAAGA +TGAATTTACACCTTTTGATGTTGTTAGACAATGCTCAGGTGTTACTTTCCAAAGTGCAGTGAAAAGAACA +ATCAAGGGTACACACCACTGGTTGTTACTCACAATTTTGACTTCACTTTTAGTTTTAGTCCAGAGTACTC +AATGGTCTTTGTTCTTTTTTTTGTATGAAAATGCCTTTTTACCTTTTGCTATGGGTATTATTGCTATGTC +TGCTTTTGCAATGATGTTTGTCAAACATAAGCATGCATTTCTCTGTTTGTTTTTGTTACCTTCTCTTGCC +ACTGTAGCTTATTTTAATATGGTCTATATGCCTGCTAGTTGGGTGATGCGTATTATGACATGGTTGGATA +TGGTTGATACTAGTTTGTCTGGTTTTAAGCTAAAAGACTGTGTTATGTATGCATCAGCTGTAGTGTTACT +AATCCTTATGACAGCAAGAACTGTGTATGATGATGGTGCTAGGAGAGTGTGGACACTTATGAATGTCTTG +ACACTCGTTTATAAAGTTTATTATGGTAATGCTTTAGATCAAGCCATTTCCATGTGGGCTCTTATAATCT +CTGTTACTTCTAACTACTCAGGTGTAGTTACAACTGTCATGTTTTTGGCCAGAGGTATTGTTTTTATGTG +TGTTGAGTATTGCCCTATTTTCTTCATAACTGGTAATACACTTCAGTGTATAATGCTAGTTTATTGTTTC +TTAGGCTATTTTTGTACTTGTTACTTTGGCCTCTTTTGTTTACTCAACCGCTACTTTAGACTGACTCTTG +GTGTTTATGATTACTTAGTTTCTACACAGGAGTTTAGATATATGAATTCACAGGGACTACTCCCACCCAA +GAATAGCATAGATGCCTTCAAACTCAACATTAAATTGTTGGGTGTTGGTGGCAAACCTTGTATCAAAGTA +GCCACTGTACAGTCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAAC +TCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAA +AGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTA +GACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAAGCTATAGCCTCAGAGTTTA +GTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGA +TTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCA +GCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTG +AGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAA +TGATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACA +ACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACAT +TTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAG +TGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCT +GCTGTCAAATTACAGAATAATGAGCTTAGTCCTGTTGCACTACGACAGATGTCTTGTGCTGCCGGTACTA +CACAAACTGCTTGCACTGATGACAATGCGTTAGCTTACTACAACACAACAAAGGGAGGTAGGTTTGTACT +TGCACTGTTATCCGATTTACAGGATTTGAAATGGGCTAGATTCCCTAAGAGTGATGGAACTGGTACTATC +TATACAGAACTGGAACCACCTTGTAGGTTTGTTACAGACACACCTAAAGGTCCTAAAGTGAAGTATTTAT +ACTTTATTAAAGGATTAAACAACCTAAATAGAGGTATGGTACTTGGTAGTTTAGCTGCCACAGTACGTCT +ACAAGCTGGTAATGCAACAGAAGTGCCTGCCAATTCAACTGTATTATCTTTCTGTGCTTTTGCTGTAGAT +GCTGCTAAAGCTTACAAAGATTATCTAGCTAGTGGGGGACAACCAATCACTAATTGTGTTAAGATGTTGT +GTACACACACTGGTACTGGTCAGGCAATAACAGTTACACCGGAAGCCAATATGGATCAAGAATCCTTTGG +TGGTGCATCGTGTTGTCTGTACTGCCGTTGCCACATAGATCATCCAAATCCTAAAGGATTTTGTGACTTA +AAAGGTAAGTATGTACAAATACCTACAACTTGTGCTAATGACCCTGTGGGTTTTACACTTAAAAACACAG +TCTGTACCGTCTGCGGTATGTGGAAAGGTTATGGCTGTAGTTGTGATCAACTCCGCGAACCCATGCTTCA +GTCAGCTGATGCACAATCGTTTTTAAACGGGTTTGCGGTGTAAGTGCAGCCCGTCTTACACCGTGCGGCA +CAGGCACTAGTACTGATGTCGTATACAGGGCTTTTGACATCTACAATGATAAAGTAGCTGGTTTTGCTAA +ATTCCTAAAAACTAATTGTTGTCGCTTCCAAGAAAAGGACGAAGATGACAATTTAATTGATTCTTACTTT +GTAGTTAAGAGACACACTTTCTCTAACTACCAACATGAAGAAACAATTTATAATTTACTTAAGGATTGTC +CAGCTGTTGCTAAACATGACTTCTTTAAGTTTAGAATAGACGGTGACATGGTACCACATATATCACGTCA +ACGTCTTACTAAATACACAATGGCAGACCTCGTCTATGCTTTAAGGCATTTTGATGAAGGTAATTGTGAC +ACATTAAAAGAAATACTTGTCACATACAATTGTTGTGATGATGATTATTTCAATAAAAAGGACTGGTATG +ATTTTGTAGAAAACCCAGATATATTACGCGTATACGCCAACTTAGGTGAACGTGTACGCCAAGCTTTGTT +AAAAACAGTACAATTCTGTGATGCCATGCGAAATGCTGGTATTGTTGGTGTACTGACATTAGATAATCAA +GATCTCAATGGTAACTGGTATGATTTCGGTGATTTCATACAAACCACGCCAGGTAGTGGAGTTCCTGTTG +TAGATTCTTATTATTCATTGTTAATGCCTATATTAACCTTGACCAGGGCTTTAACTGCAGAGTCACATGT +TGACACTGACTTAACAAAGCCTTACATTAAGTGGGATTTGTTAAAATATGACTTCACGGAAGAGAGGTTA +AAACTCTTTGACCGTTATTTTAAATATTGGGATCAGACATACCACCCAAATTGTGTTAACTGTTTGGATG +ACAGATGCATTCTGCATTGTGCAAACTTTAATGTTTTATTCTCTACAGTGTTCCCACCTACAAGTTTTGG +ACCACTAGTGAGAAAAATATTTGTTGATGGTGTTCCATTTGTAGTTTCAACTGGATACCACTTCAGAGAG +CTAGGTGTTGTACATAATCAGGATGTAAACTTACATAGCTCTAGACTTAGTTTTAAGGAATTACTTGTGT +ATGCTGCTGACCCTGCTATGCACGCTGCTTCTGGTAATCTATTACTAGATAAACGCACTACGTGCTTTTC +AGTAGCTGCACTTACTAACAATGTTGCTTTTCAAACTGTCAAACCCGGTAATTTTAACAAAGACTTCTAT +GACTTTGCTGTGTCTAAGGGTTTCTTTAAGGAAGGAAGTTCTGTTGAATTAAAACACTTCTTCTTTGCTC +AGGATGGTAATGCTGCTATCAGCGATTATGACTACTATCGTTATAATCTACCAACAATGTGTGATATCAG +ACAACTACTATTTGTAGTTGAAGTTGTTGATAAGTACTTTGATTGTTACGATGGTGGCTGTATTAATGCT +AACCAAGTCATCGTCAACAACCTAGACAAATCAGCTGGTTTTCCATTTAATAAATGGGGTAAGGCTAGAC +TTTATTATGATTCAATGAGTTATGAGGATCAAGATGCACTTTTCGCATATACAAAACGTAATGTCATCCC +TACTATAACTCAAATGAATCTTAAGTATGCCATTAGTGCAAAGAATAGAGCTCGCACCGTAGCTGGTGTC +TCTATCTGTAGTACTATGACCAATAGACAGTTTCATCAAAAATTATTGAAATCAATAGCCGCCACTAGAG +GAGCTACTGTAGTAATTGGAACAAGCAAATTCTATGGTGGTTGGCACAACATGTTAAAAACTGTTTATAG +TGATGTAGAAAACCCTCACCTTATGGGTTGGGATTATCCTAAATGTGATAGAGCCATGCCTAACATGCTT +AGAATTATGGCCTCACTTGTTCTTGCTCGCAAACATACAACGTGTTGTAGCTTGTCACACCGTTTCTATA +GATTAGCTAATGAGTGTGCTCAAGTATTGAGTGAAATGGTCATGTGTGGCGGTTCACTATATGTTAAACC +AGGTGGAACCTCATCAGGAGATGCCACAACTGCTTATGCTAATAGTGTTTTTAACATTTGTCAAGCTGTC +ACGGCCAATGTTAATGCACTTTTATCTACTGATGGTAACAAAATTGCCGATAAGTATGTCCGCAATTTAC +AACACAGACTTTATGAGTGTCTCTATAGAAATAGAGATGTTGACACAGACTTTGTGAATGAGTTTTACGC +ATATTTGCGTAAACATTTCTCAATGATGATACTCTCTGACGATGCTGTTGTGTGTTTCAATAGCACTTAT +GCATCTCAAGGTCTAGTGGCTAGCATAAAGAACTTTAAGTCAGTTCTTTATTATCAAAACAATGTTTTTA +TGTCTGAAGCAAAATGTTGGACTGAGACTGACCTTACTAAAGGACCTCATGAATTTTGCTCTCAACATAC +AATGCTAGTTAAACAGGGTGATGATTATGTGTACCTTCCTTACCCAGATCCATCAAGAATCCTAGGGGCC +GGCTGTTTTGTAGATGATATCGTAAAAACAGATGGTACACTTATGATTGAACGGTTCGTGTCTTTAGCTA +TAGATGCTTACCCACTTACTAAACATCCTAATCAGGAGTATGCTGATGTCTTTCATTTGTACTTACAATA +CATAAGAAAGCTACATGATGAGTTAACAGGACACATGTTAGACATGTATTCTGTTATGCTTACTAATGAT +AACACTTCAAGGTATTGGGAACCTGAGTTTTATGAGGCTATGTACACACCGCATACAGTCTTACAGGCTG +TTGGGGCTTGTGTTCTTTGCAATTCACAGACTTCATTAAGATGTGGTGCTTGCATACGTAGACCATTCTT +ATGTTGTAAATGCTGTTACGACCATGTCATATCAACATCACATAAATTAGTCTTGTCTGTTAATCCGTAT +GTTTGCAATGCTCCAGGTTGTGATGTCACAGATGTGACTCAACTTTACTTAGGAGGTATGAGCTATTATT +GTAAATCACATAAACCACCCATTAGTTTTCCATTGTGTGCTAATGGACAAGTTTTTGGTTTATATAAAAA +TACATGTGTTGGTAGCGATAATGTTACTGACTTTAATGCAATTGCAACATGTGACTGGACAAATGCTGGT +GATTACATTTTAGCTAACACCTGTACTGAAAGACTCAAGCTTTTTGCAGCAGAAACGCTCAAAGCTACTG +AGGAGACATTTAAACTGTCTTATGGTATTGCTACTGTACGTGAAGTGCTGTCTGACAGAGAATTACATCT +TTCATGGGAAGTTGGTAAACCTAGACCACCACTTAACCGAAATTATGTCTTTACTGGTTATCGTGTAACT +AAAAACAGTAAAGTACAAATAGGAGAGTACACCTTTGAAAAAGGTGACTATGGTGATGCTGTTGTTTACC +GAGGTACAACAACTTACAAATTAAATGTTGGTGATTATTTTGTGCTGACATCACATACAGTAATGCCATT +AAGTGCACCTACACTAGTGCCACAAGAGCACTATGTTAGAATTACTGGCTTATACCCAACACTCAATATC +TCAGATGAGTTTTCTAGCAATGTTGCAAATTATCAAAAGGTTGGTATGCAAAAGTATTCTACACTCCAGG +GACCACCTGGTACTGGTAAGAGTCATTTTGCTATTGGCCTAGCTCTCTACTACCCTTCTGCTCGCATAGT +GTATACAGCTTGCTCTCATGCCGCTGTTGATGCACTATGTGAGAAGGCATTAAAATATTTGCCTATAGAT +AAATGTAGTAGAATTATACCTGCACGTGCTCGTGTAGAGTGTTTTGATAAATTCAAAGTGAATTCAACAT +TAGAACAGTATGTCTTTTGTACTGTAAATGCATTGCCTGAGACGACAGCAGATATAGTTGTCTTTGATGA +AATTTCAATGGCCACAAATTATGATTTGAGTGTTGTCAATGCCAGATTACGTGCTAAGCACTATGTGTAC +ATTGGCGACCCTGCTCAATTACCTGCACCACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATT +TCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCC +TGCTGAAATTGTTGACACTGTGAGTGCTTTGGTTTATGATAATAAGCTTAAAGCACATAAAGACAAATCA +GCTCAATGCTTTAAAATGTTTTATAAGGGTGTTATCACGCATGATGTTTCATCTGCAATTAACAGGCCAC +AAATAGGCGTGGTAAGAGAATTCCTTACACGTAACCCTGCTTGGAGAAAAGCTGTCTTTATTTCACCTTA +TAATTCACAGAATGCTGTAGCCTCAAAGATTTTGGGACTACCAACTCAAACTGTTGATTCATCACAGGGC +TCAGAATATGACTATGTCATATTCACTCAAACCACTGAAACAGCTCACTCTTGTAATGTAAACAGATTTA +ATGTTGCTATTACCAGAGCAAAAGTAGGCATACTTTGCATAATGTCTGATAGAGACCTTTATGACAAGTT +GCAATTTACAAGTCTTGAAATTCCACGTAGGAATGTGGCAACTTTACAAGCTGAAAATGTAACAGGACTC +TTTAAAGATTGTAGTAAGGTAATCACTGGGTTACATCCTACACAGGCACCTACACACCTCAGTGTTGACA +CTAAATTCAAAACTGAAGGTTTATGTGTTGACATACCTGGCATACCTAAGGACATGACCTATAGAAGACT +CATCTCTATGATGGGTTTTAAAATGAATTATCAAGTTAATGGTTACCCTAACATGTTTATCACCCGCGAA +GAAGCTATAAGACATGTACGTGCATGGATTGGCTTCGATGTCGAGGGGTGTCATGCTACTAGAGAAGCTG +TTGGTACCAATTTACCTTTACAGCTAGGTTTTTCTACAGGTGTTAACCTAGTTGCTGTACCTACAGGTTA +TGTTGATACACCTAATAATACAGATTTTTCCAGAGTTAGTGCTAAACCACCGCCTGGAGATCAATTTAAA +CACCTCATACCACTTATGTACAAAGGACTTCCTTGGAATGTAGTGCGTATAAAGATTGTACAAATGTTAA +GTGACACACTTAAAAATCTCTCTGACAGAGTCGTATTTGTCTTATGGGCACATGGCTTTGAGTTGACATC +TATGAAGTATTTTGTGAAAATAGGACCTGAGCGCACCTGTTGTCTATGTGATAGACGTGCCACATGCTTT +TCCACTGCTTCAGACACTTATGCCTGTTGGCATCATTCTATTGGATTTGATTACGTCTATAATCCGTTTA +TGATTGATGTTCAACAATGGGGTTTTACAGGTAACCTACAAAGCAACCATGATCTGTATTGTCAAGTCCA +TGGTAATGCACATGTAGCTAGTTGTGATGCAATCATGACTAGGTGTCTAGCTGTCCACGAGTGCTTTGTT +AAGCGTGTTGACTGGACTATTGAATATCCTATAATTGGTGATGAACTGAAGATTAATGCGGCTTGTAGAA +AGGTTCAACACATGGTTGTTAAAGCTGCATTATTAGCAGACAAATTCCCAGTTCTTCACGACATTGGTAA +CCCTAAAGCTATTAAGTGTGTACCTCAAGCTGATGTAGAATGGAAGTTCTATGATGCACAGCCTTGTAGT +GACAAAGCTTATAAAATAGAAGAATTATTCTATTCTTATGCCACACATTCTGACAAATTCACAGATGGTG +TATGCCTATTTTGGAATTGCAATGTCGATAGATATCCTGCTAATTCCATTGTTTGTAGATTTGACACTAG +AGTGCTATCTAACCTTAACTTGCCTGGTTGTGATGGTGGCAGTTTGTATGTAAATAAACATGCATTCCAC +ACACCAGCTTTTGATAAAAGTGCTTTTGTTAATTTAAAACAATTACCATTTTTCTATTACTCTGACAGTC +CATGTGAGTCTCATGGAAAACAAGTAGTGTCAGATATAGATTATGTACCACTAAAGTCTGCTACGTGTAT +AACACGTTGCAATTTAGGTGGTGCTGTCTGTAGACATCATGCTAATGAGTACAGATTGTATCTCGATGCT +TATAACATGATGATCTCAGCTGGCTTTAGCTTGTGGGTTTACAAACAATTTGATACTTATAACCTCTGGA +ACACTTTTACAAGACTTCAGAGTTTAGAAAATGTGGCTTTTAATGTTGTAAATAAGGGACACTTTGATGG +ACAACAGGGTGAAGTACCAGTTTCTATCATTAATAACACTGTTTACACAAAAGTTGATGGTGTTGATGTA +GAATTGTTTGAAAATAAAACAACATTACCTGTTAATGTAGCATTTGAGCTTTGGGCTAAGCGCAACATTA +AACCAGTACCAGAGGTGAAAATACTCAATAATTTGGGTGTGGACATTGCTGCTAATACTGTGATCTGGGA +CTACAAAAGAGATGCTCCAGCACATATATCTACTATTGGTGTTTGTTCTATGACTGACATAGCCAAGAAA +CCAACTGAAACGATTTGTGCACCACTCACTGTCTTTTTTGATGGTAGAGTTGATGGTCAAGTAGACTTAT +TTAGAAATGCCCGTAATGGTGTTCTTATTACAGAAGGTAGTGTTAAAGGTTTACAACCATCTGTAGGTCC +CAAACAAGCTAGTCTTAATGGAGTCACATTAATTGGAGAAGCCGTAAAAACACAGTTCAATTATTATAAG +AAAGTTGATGGTGTTGTCCAACAATTACCTGAAACTTACTTTACTCAGAGTAGAAATTTACAAGAATTTA +AACCCAGGAGTCAAATGGAAATTGATTTCTTAGAATTAGCTATGGATGAATTCATTGAACGGTATAAATT +AGAAGGCTATGCCTTCGAACATATCGTTTATGGAGATTTTAGTCATAGTCAGTTAGGTGGTTTACATCTA +CTGATTGGACTAGCTAAACGTTTTAAGGAATCACCTTTTGAATTAGAAGATTTTATTCCTATGGACAGTA +CAGTTAAAAACTATTTCATAACAGATGCGCAAACAGGTTCATCTAAGTGTGTGTGTTCTGTTATTGATTT +ATTACTTGATGATTTTGTTGAAATAATAAAATCCCAAGATTTATCTGTAGTTTCTAAGGTTGTCAAAGTG +ACTATTGACTATACAGAAATTTCATTTATGCTTTGGTGTAAAGATGGCCATGTAGAAACATTTTACCCAA +AATTACAATCTAGTCAAGCGTGGCAACCGGGTGTTGCTATGCCTAATCTTTACAAAATGCAAAGAATGCT +ATTAGAAAAGTGTGACCTTCAAAATTATGGTGATAGTGCAACATTACCTAAAGGCATAATGATGAATGTC +GCAAAATATACTCAACTGTGTCAATATTTAAACACATTAACATTAGCTGTACCCTATAATATGAGAGTTA +TACATTTTGGTGCTGGTTCTGATAAAGGAGTTGCACCAGGTACAGCTGTTTTAAGACAGTGGTTGCCTAC +GGGTACGCTGCTTGTCGATTCAGATCTTAATGACTTTGTCTCTGATGCAGATTCAACTTTGATTGGTGAT +TGTGCAACTGTACATACAGCTAATAAATGGGATCTCATTATTAGTGATATGTACGACCCTAAGACTAAAA +ATGTTACAAAAGAAAATGACTCTAAAGAGGGTTTTTTCACTTACATTTGTGGGTTTATACAACAAAAGCT +AGCTCTTGGAGGTTCCGTGGCTATAAAGATAACAGAACATTCTTGGAATGCTGATCTTTATAAGCTCATG +GGACACTTCGCATGGTGGACAGCCTTTGTTACTAATGTGAATGCGTCATCATCTGAAGCATTTTTAATTG +GATGTAATTATCTTGGCAAACCACGCGAACAAATAGATGGTTATGTCATGCATGCAAATTACATATTTTG +GAGGAATACAAATCCAATTCAGTTGTCTTCCTATTCTTTATTTGACATGAGTAAATTTCCCCTTAAATTA +AGGGGTACTGCTGTTATGTCTTTAAAAGAAGGTCAAATCAATGATATGATTTTATCTCTTCTTAGTAAAG +GTAGACTTATAATTAGAGAAAACAACAGAGTTGTTATTTCTAGTGATGTTCTTGTTAACAACTAAACGAA +CAATGTTTGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACCAGAACTCA +ATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGACAAAGTTTTCAGATCCTCA +GTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCCAATGTTACTTGGTTCCATGCTATACATG +TCTCTGGGACCAATGGTACTAAGAGGTTTGATAACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGC +TTCCACTGAGAAGTCTAACATAATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCC +CTACTTATTGTTAATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATGATCCAT +TTTTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTATTCTAGTGC +GAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAAGGAAAACAGGGTAATTTC +AAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTATTTTAAAATATATTCTAAGCACACGCCTA +TTAATTTAGTGCGTGATCTCCCTCAGGGTTTTTCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTAT +TAACATCACTAGGTTTCAAACTTTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCA +GGTTGGACAGCTGGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATA +ATGAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAGTGTACGTT +GAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTCCAACCAACAGAATCTATT +GTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAAGTTTTTAACGCCACCAGATTTGCATCTG +TTTATGCTTGGAACAGGAAGAGAATCAGCAACTGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATC +ATTTTCCACTTTTAAGTGTTATGGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTAT +GCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTG +ATTATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAATCTTGATTC +TAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAATCTCAAACCTTTTGAGAGA +GATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGTAATGGTGTTGAAGGTTTTAATTGTTACT +TTCCTTTACAATCATATGGTTTCCAACCCACTAATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACT +TTCTTTTGAACTTCTACATGCACCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAAC +AAATGTGTCAATTTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTC +TGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAGACACTTGA +GATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCAGGAACAAATACTTCTAAC +CAGGTTGCTGTTCTTTATCAGGATGTTAACTGCACAGAAGTCCCTGTTGCTATTCATGCAGATCAACTTA +CTCCTACTTGGCGTGTTTATTCTACAGGTTCTAATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGC +TGAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACT +CAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTG +GTGCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATTAGTGTTAC +CACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATGTACATTTGTGGTGATTCA +ACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGTACACAATTAAACCGTGCTTTAACTGGAA +TAGCTGTTGAACAAGACAAAAACACCCAAGAAGTTTTTGCACAAGTCAAACAAATTTACAAAACACCACC +AATTAAAGATTTTGGTGGTTTTAATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCA +TTTATTGAAGATCTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATT +GCCTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTTTTGCCACC +TTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGTACAATCACTTCTGGTTGG +ACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATGCAAATGGCTTATAGGTTTAATGGTATTG +GAGTTACACAGAATGTTCTCTATGAGAACCAAAAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAA +AATTCAAGACTCACTTTCTTCCACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCA +CAAGCTTTAAACACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATA +TCCTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGACTTCAAAG +TTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCTTCTGCTAATCTTGCTGCT +ACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTTGATTTTTGTGGAAAGGGCTATCATCTTA +TGTCCTTCCCTCAGTCAGCACCTCATGGTGTAGTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAA +GAACTTCACAACTGCTCCTGCCATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTT +TCAAATGGCACACACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACA +CATTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCTTTGCAACC +TGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACATCACCAGATGTTGATTTA +GGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAAAAAGAAATTGACCGCCTCAATGAGGTTG +CCAAGAATTTAAATGAATCTCTCATCGATCTCCAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCC +ATGGTACATTTGGCTAGGTTTTATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGT +ATGACCAGTTGCTGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACG +ACTCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACATAAACGAACTTATGGATTTGTTTATGAGA +ATCTTCACAATTGGAACTGTAACTTTGAAGCAAGGTGAAATCAAGGATGCTACTCCTTCAGATTTTGTTC +GCGCTACTGCAACGATACCGATACAAGCCTCACTCCCTTTCGGATGGCTTATTGTTGGCGTTGCACTTCT +TGCTGTTTTTCAGAGCGCTTCCAAAATCATAACCCTCAAAAAGAGATGGCAACTAGCACTCTCCAAGGGT +GTTCACTTTGTTTGCAACTTGCTGTTGTTGTTTGTAACAGTTTACTCACACCTTTTGCTCGTTGCTGCTG +GCCTTGAAGCCCCTTTTCTCTATCTTTATGCTTTAGTCTACTTCTTGCAGAGTATAAACTTTGTAAGAAT +AATAATGAGGCTTTGGCTTTGCTGGAAATGCCGTTCCAAAAACCCATTACTTTATGATGCCAACTATTTT +CTTTGCTGGCATACTAATTGTTACGACTATTGTATACCTTACAATAGTGTAACTTCTTCAATTGTCATTA +CTTCAGGTGATGGCACAACAAGTCCTATTTCTGAACATGACTACCAGATTGGTGGTTATACTGAAAAATG +GGAATCTGGAGTAAAAGACTGTGTTGTATTACACAGTTACTTCACTTCAGACTATTACCAGCTGTACTCA +ACTCAATTGAGTACAGACACTGGTGTTGAACATGTTACCTTCTTCATCTACAATAAAATTGTTGATGAGC +CTGAAGAACATGTCCAAATTCACACAATCGACGGTTCATCCGGAGTTGTTAATCCAGTAATGGAACCAAT +TTATGATGAACCGACGACGACTACTAGCGTGCCTTTGTAAGCACAAGCTGATGAGTACGAACTTATGTAC +TCATTCGTTTCGGAAGAGACAGGTACGTTAATAGTTAATAGCGTACTTCTTTTTCTTGCTTTCGTGGTAT +TCTTGCTAGTTACACTAGCCATCCTTACTGCGCTTCGATTGTGTGCGTACTGCTGCAATATTGTTAACGT +GAGTCTTGTAAAACCTTCTTTTTACGTTTACTCTCGTGTTAAAAATCTGAATTCTTCTAGAGTTCCTGAT +CTTCTGGTCTAAACGAACTAAATATTATATTAGTTTTTCTGTTTGGAACTTTAATTTTAGCCATGGCAGA +TTCCAACGGTACTATTACCGTTGAAGAGCTTAAAAAGCTCCTTGAACAATGGAACCTAGTAATAGGTTTC +CTATTCCTTACATGGATTTGTCTTCTACAATTTGCCTATGCCAACAGGAATAGGTTTTTGTATATAATTA +AGTTAATTTTCCTCTGGCTGTTATGGCCAGTAACTTTAGCTTGTTTTGTGCTTGCTGCTGTTTACAGAAT +AAATTGGATCACCGGTGGAATTGCTATCGCAATGGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTC +ATTGCTTCTTTCAGACTGTTTGCGCGTACGCGTTCCATGTGGTCATTCAATCCAGAAACTAACATTCTTC +TCAACGTGCCACTCCATGGCACTATTCTGACCAGACCGCTTCTAGAAAGTGAACTCGTAATCGGAGCTGT +GATCCTTCGTGGACATCTTCGTATTGCTGGACACCATCTAGGACGCTGTGACATCAAGGACCTGCCTAAA +GAAATCACTGTTGCTACATCACGAACGCTTTCTTATTACAAATTGGGAGCTTCGCAGCGTGTAGCAGGTG +ACTCAGGTTTTGCTGCATACAGTCGCTACAGGATTGGCAACTATAAATTAAACACAGACCATTCCAGTAG +CAGTGACAATATTGCTTTGCTTGTACAGTAAGTGACAACAGATGTTTCATCTCGTTGACTTTCAGGTTAC +TATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATA +AACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAAC +CAATGGAGATTGATTAAACGAACATGAAAATTATTCTTTTCTTGGCACTGATAACACTCGCTACTTGTGA +GCTTTATCACTACCAAGAGTGTGTTAGAGGTACAACAGTACTTTTAAAAGAACCTTGCTCTTCTGGAACA +TACGAGGGCAATTCACCATTTCATCCTCTAGCTGATAACAAATTTGCACTGACTTGCTTTAGCACTCAAT +TTGCTTTTGCTTGTCCTGACGGCGTAAAACACGTCTATCAGTTACGTGCCAGATCAGTTTCACCTAAACT +GTTCATCAGACAAGAGGAAGTTCAAGAACTTTACTCTCCAATTTTTCTTATTGTTGCGGCAATAGTGTTT +ATAACACTTTGCTTCACACTCAAAAGAAAGACAGAATGATTGAACTTTCATTAATTGACTTCTATTTGTG +CTTTTTAGCCTTTCTGCTATTCCTTGTTTTAATTATGCTTATTATCTTTTGGTTCTCACTTGAACTGCAA +GATCATAATGAAACTTGTCACGCCTAAACGAACATGAAATTTCTTGTTTTCTTAGGAATCATCACAACTG +TAGCTGCATTTCACCAAGAATGTAGTTTACAGTCATGTACTCAACATCAACCATATGTAGTTGATGACCC +GTGTCCTATTCACTTCTATTCTAAATGGTATATTAGAGTAGGAGCTAGAAAATCAGCACCTTTAATTGAA +TTGTGCGTGGATGAGGCTGGTTCTAAATCACCCATTCAGTACATCGATATCGGTAATTATACAGTTTCCT +GTTTACCTTTTACAATTAATTGCCAGGAACCTAAATTGGGTAGTCTTGTAGTGCGTTGTTCGTTCTATGA +AGACTTTTTAGAGTATCATGACGTTCGTGTTGTTTTAGATTTCATCTAAACGAACAAACTAAAATGTCTG +ATAATGGACCCCAAAATCAGCGAAATGCACCCCGCATTACGTTTGGTGGACCCTCAGATTCAACTGGCAG +TAACCAGAATGGAGAACGCAGTGGGGCGCGATCAAAACAACGTCGGCCCCAAGGTTTACCCAATAATACT +GCGTCTTGGTTCACCGCTCTCACTCAACATGGCAAGGAAGACCTTAAATTCCCTCGAGGACAAGGCGTTC +CAATTAACACCAATAGCAGTCCAGATGACCAAATTGGCTACTACCGAAGAGCTACCAGACGAATTCGTGG +TGGTGACGGTAAAATGAAAGATCTCAGTCCAAGATGGTATTTCTACTACCTAGGAACTGGGCCAGAAGCT +GGACTTCCCTATGGTGCTAACAAAGACGGCATCATATGGGTTGCAACTGAGGGAGCCTTGAATACACCAA +AAGATCACATTGGCACCCGCAATCCTGCTAACAATGCTGCAATCGTGCTACAACTTCCTCAAGGAACAAC +ATTGCCAAAAGGCTTCTACGCAGAAGGGAGCAGAGGCGGCAGTCAAGCCTCTTCTCGTTCCTCATCACGT +AGTCGCAACAGTTCAAGAAATTCAACTCCAGGCAGCAGTAGGGGAACTTCTCCTGCTAGAATGGCTGGCA +ATGGCGGTGATGCTGCTCTTGCTTTGCTGCTGCTTGACAGATTGAACCAGCTTGAGAGCAAAATGTCTGG +TAAAGGCCAACAACAACAAGGCCAAACTGTCACTAAGAAATCTGCTGCTGAGGCTTCTAAGAAGCCTCGG +CAAAAACGTACTGCCACTAAAGCATACAATGTAACACAAGCTTTCGGCAGACGTGGTCCAGAACAAACCC +AAGGAAATTTTGGGGACCAGGAACTAATCAGACAAGGAACTGATTACAAACATTGGCCGCAAATTGCACA +ATTTGCCCCCAGCGCTTCAGCGTTCTTCGGAATGTCGCGCATTGGCATGGAAGTCACACCTTCGGGAACG +TGGTTGACCTACACAGGTGCCATCAAATTGGATGACAAAGATCCAAATTTCAAAGATCAAGTCATTTTGC +TGAATAAGCATATTGACGCATACAAAACATTCCCACCAACAGAGCCTAAAAAGGACAAAAAGAAGAAGGC +TGATGAAACTCAAGCCTTACCGCAGAGACAGAAGAAACAGCAAACTGTGACTCTTCTTCCTGCTGCAGAT +TTGGATGATTTCTCCAAACAATTGCAACAATCCATGAGCAGTGCTGACTCAACTCAGGCCTAAACTCATG +CAGACCACACAAGGCAGATGGGCTATATAAACGTTTTCGCTTTTCCGTTTACGATATATAGTCTACTCTT +GTGCAGAATGAATTCTCGTAACTACATAGCACAAGTAGATGTAGTTAACTTTAATCTCACATAGCAATCT +TTAATCAGTGTGTAACATTAGGGAGGACTTGAAAGAGCCACCACATTTTCACCGAGGCCACGCGGAGTAC +GATCGAGTGTACAGTGAACAATGCTAGGGAGAGCTGCCTATATGGAAGAGCCCTAATGTGTAAAATTAAT +TTTAGTAGTGCTATCCCCATGTGATTTTAATAGCTTCTTAGGAGAATGACAAAAAAAAAAAAAAAAAAAA +AAAAAAAAAAAAA diff --git a/test/data/broken/info-yml/missing-field/info.yml b/test/data/broken/info-yml/missing-field/info.yml new file mode 100644 index 0000000..0fc1a71 --- /dev/null +++ b/test/data/broken/info-yml/missing-field/info.yml @@ -0,0 +1,21 @@ +name: artic +amplicon_size: 400 +version: v4.1 +organism: sars-cov-2 +aliases: +- ARTIC/V4.1 +developers: +- ARTIC network +vendors: +- organisation_name: IDT + kit_name: '10011442' +- organisation_name: Eurofins + home_page: https://eurofinsgenomics.com +definition_url: https://github.com/pha4ge/primer-schemes/tree/main/sars-cov-2/artic/v4.1 +source_url: https://github.com/quick-lab/primerschemes/tree/main/primerschemes/artic-sars-cov-2/400/v4.1.0 +citations: +- https://doi.org/10.1101%2F2020.09.04.283077 +derived_from: artic-v4 +license: CC-BY-SA-4.0 +primer_checksum: primaschema:8eaf6a2fb31f602a +reference_checksum: primaschema:b1acd7163146bf17 diff --git a/test/data/broken/info-yml/missing-field/primer.bed b/test/data/broken/info-yml/missing-field/primer.bed new file mode 100644 index 0000000..3279bff --- /dev/null +++ b/test/data/broken/info-yml/missing-field/primer.bed @@ -0,0 +1,4 @@ +MN908947.3 25 50 SARS-CoV-2_1_LEFT_1 1 + AACAAACCAACCAACTTTCGATCTC +MN908947.3 408 431 SARS-CoV-2_1_RIGHT_1 1 - CTTCTACTAAGCCACAAGTGCCA +MN908947.3 324 344 SARS-CoV-2_2_LEFT_1 2 + TTTACAGGTTCGCGACGTGC +MN908947.3 705 727 SARS-CoV-2_2_RIGHT_1 2 - ATAAGGATCAGTGCCAAGCTCG \ No newline at end of file diff --git a/test/data/broken/info-yml/missing-field/reference.fasta b/test/data/broken/info-yml/missing-field/reference.fasta new file mode 100644 index 0000000..e1cfd92 --- /dev/null +++ b/test/data/broken/info-yml/missing-field/reference.fasta @@ -0,0 +1,429 @@ +>MN908947.3 +ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAA +CGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAAC +TAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTG +TTGCAGCCGATCATCAGCACATCTAGGTTTCGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTC +CCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTAC +GTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGG +CTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAAACGTTCGGAT +GCTCGAACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACTCGAAGGCATTCAGTACGGTC +GTAGTGGTGAGACACTTGGTGTCCTTGTCCCTCATGTGGGCGAAATACCAGTGGCTTACCGCAAGGTTCT +TCTTCGTAAGAACGGTAATAAAGGAGCTGGTGGCCATAGTTACGGCGCCGATCTAAAGTCATTTGACTTA +GGCGACGAGCTTGGCACTGATCCTTATGAAGATTTTCAAGAAAACTGGAACACTAAACATAGCAGTGGTG +TTACCCGTGAACTCATGCGTGAGCTTAACGGAGGGGCATACACTCGCTATGTCGATAACAACTTCTGTGG +CCCTGATGGCTACCCTCTTGAGTGCATTAAAGACCTTCTAGCACGTGCTGGTAAAGCTTCATGCACTTTG +TCCGAACAACTGGACTTTATTGACACTAAGAGGGGTGTATACTGCTGCCGTGAACATGAGCATGAAATTG +CTTGGTACACGGAACGTTCTGAAAAGAGCTATGAATTGCAGACACCTTTTGAAATTAAATTGGCAAAGAA +ATTTGACACCTTCAATGGGGAATGTCCAAATTTTGTATTTCCCTTAAATTCCATAATCAAGACTATTCAA +CCAAGGGTTGAAAAGAAAAAGCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCCAGTTGCGTCAC +CAAATGAATGCAACCAAATGTGCCTTTCAACTCTCATGAAGTGTGATCATTGTGGTGAAACTTCATGGCA +GACGGGCGATTTTGTTAAAGCCACTTGCGAATTTTGTGGCACTGAGAATTTGACTAAAGAAGGTGCCACT +ACTTGTGGTTACTTACCCCAAAATGCTGTTGTTAAAATTTATTGTCCAGCATGTCACAATTCAGAAGTAG +GACCTGAGCATAGTCTTGCCGAATACCATAATGAATCTGGCTTGAAAACCATTCTTCGTAAGGGTGGTCG +CACTATTGCCTTTGGAGGCTGTGTGTTCTCTTATGTTGGTTGCCATAACAAGTGTGCCTATTGGGTTCCA +CGTGCTAGCGCTAACATAGGTTGTAACCATACAGGTGTTGTTGGAGAAGGTTCCGAAGGTCTTAATGACA +ACCTTCTTGAAATACTCCAAAAAGAGAAAGTCAACATCAATATTGTTGGTGACTTTAAACTTAATGAAGA +GATCGCCATTATTTTGGCATCTTTTTCTGCTTCCACAAGTGCTTTTGTGGAAACTGTGAAAGGTTTGGAT +TATAAAGCATTCAAACAAATTGTTGAATCCTGTGGTAATTTTAAAGTTACAAAAGGAAAAGCTAAAAAAG +GTGCCTGGAATATTGGTGAACAGAAATCAATACTGAGTCCTCTTTATGCATTTGCATCAGAGGCTGCTCG +TGTTGTACGATCAATTTTCTCCCGCACTCTTGAAACTGCTCAAAATTCTGTGCGTGTTTTACAGAAGGCC +GCTATAACAATACTAGATGGAATTTCACAGTATTCACTGAGACTCATTGATGCTATGATGTTCACATCTG +ATTTGGCTACTAACAATCTAGTTGTAATGGCCTACATTACAGGTGGTGTTGTTCAGTTGACTTCGCAGTG +GCTAACTAACATCTTTGGCACTGTTTATGAAAAACTCAAACCCGTCCTTGATTGGCTTGAAGAGAAGTTT +AAGGAAGGTGTAGAGTTTCTTAGAGACGGTTGGGAAATTGTTAAATTTATCTCAACCTGTGCTTGTGAAA +TTGTCGGTGGACAAATTGTCACCTGTGCAAAGGAAATTAAGGAGAGTGTTCAGACATTCTTTAAGCTTGT +AAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGCCTTGAATTTA +GGTGAAACATTTGTCACGCACTCAAAGGGATTGTACAGAAAGTGTGTTAAATCCAGAGAAGAAACTGGCC +TACTCATGCCTCTAAAAGCCCCAAAAGAAATTATCTTCTTAGAGGGAGAAACACTTCCCACAGAAGTGTT +AACAGAGGAAGTTGTCTTGAAAACTGGTGATTTACAACCATTAGAACAACCTACTAGTGAAGCTGTTGAA +GCTCCATTGGTTGGTACACCAGTTTGTATTAACGGGCTTATGTTGCTCGAAATCAAAGACACAGAAAAGT +ACTGTGCCCTTGCACCTAATATGATGGTAACAAACAATACCTTCACACTCAAAGGCGGTGCACCAACAAA +GGTTACTTTTGGTGATGACACTGTGATAGAAGTGCAAGGTTACAAGAGTGTGAATATCACTTTTGAACTT +GATGAAAGGATTGATAAAGTACTTAATGAGAAGTGCTCTGCCTATACAGTTGAACTCGGTACAGAAGTAA +ATGAGTTCGCCTGTGTTGTGGCAGATGCTGTCATAAAAACTTTGCAACCAGTATCTGAATTACTTACACC +ACTGGGCATTGATTTAGATGAGTGGAGTATGGCTACATACTACTTATTTGATGAGTCTGGTGAGTTTAAA +TTGGCTTCACATATGTATTGTTCTTTCTACCCTCCAGATGAGGATGAAGAAGAAGGTGATTGTGAAGAAG +AAGAGTTTGAGCCATCAACTCAATATGAGTATGGTACTGAAGATGATTACCAAGGTAAACCTTTGGAATT +TGGTGCCACTTCTGCTGCTCTTCAACCTGAAGAAGAGCAAGAAGAAGATTGGTTAGATGATGATAGTCAA +CAAACTGTTGGTCAACAAGACGGCAGTGAGGACAATCAGACAACTACTATTCAAACAATTGTTGAGGTTC +AACCTCAATTAGAGATGGAACTTACACCAGTTGTTCAGACTATTGAAGTGAATAGTTTTAGTGGTTATTT +AAAACTTACTGACAATGTATACATTAAAAATGCAGACATTGTGGAAGAAGCTAAAAAGGTAAAACCAACA +GTGGTTGTTAATGCAGCCAATGTTTACCTTAAACATGGAGGAGGTGTTGCAGGAGCCTTAAATAAGGCTA +CTAACAATGCCATGCAAGTTGAATCTGATGATTACATAGCTACTAATGGACCACTTAAAGTGGGTGGTAG +TTGTGTTTTAAGCGGACACAATCTTGCTAAACACTGTCTTCATGTTGTCGGCCCAAATGTTAACAAAGGT +GAAGACATTCAACTTCTTAAGAGTGCTTATGAAAATTTTAATCAGCACGAAGTTCTACTTGCACCATTAT +TATCAGCTGGTATTTTTGGTGCTGACCCTATACATTCTTTAAGAGTTTGTGTAGATACTGTTCGCACAAA +TGTCTACTTAGCTGTCTTTGATAAAAATCTCTATGACAAACTTGTTTCAAGCTTTTTGGAAATGAAGAGT +GAAAAGCAAGTTGAACAAAAGATCGCTGAGATTCCTAAAGAGGAAGTTAAGCCATTTATAACTGAAAGTA +AACCTTCAGTTGAACAGAGAAAACAAGATGATAAGAAAATCAAAGCTTGTGTTGAAGAAGTTACAACAAC +TCTGGAAGAAACTAAGTTCCTCACAGAAAACTTGTTACTTTATATTGACATTAATGGCAATCTTCATCCA +GATTCTGCCACTCTTGTTAGTGACATTGACATCACTTTCTTAAAGAAAGATGCTCCATATATAGTGGGTG +ATGTTGTTCAAGAGGGTGTTTTAACTGCTGTGGTTATACCTACTAAAAAGGCTGGTGGCACTACTGAAAT +GCTAGCGAAAGCTTTGAGAAAAGTGCCAACAGACAATTATATAACCACTTACCCGGGTCAGGGTTTAAAT +GGTTACACTGTAGAGGAGGCAAAGACAGTGCTTAAAAAGTGTAAAAGTGCCTTTTACATTCTACCATCTA +TTATCTCTAATGAGAAGCAAGAAATTCTTGGAACTGTTTCTTGGAATTTGCGAGAAATGCTTGCACATGC +AGAAGAAACACGCAAATTAATGCCTGTCTGTGTGGAAACTAAAGCCATAGTTTCAACTATACAGCGTAAA +TATAAGGGTATTAAAATACAAGAGGGTGTGGTTGATTATGGTGCTAGATTTTACTTTTACACCAGTAAAA +CAACTGTAGCGTCACTTATCAACACACTTAACGATCTAAATGAAACTCTTGTTACAATGCCACTTGGCTA +TGTAACACATGGCTTAAATTTGGAAGAAGCTGCTCGGTATATGAGATCTCTCAAAGTGCCAGCTACAGTT +TCTGTTTCTTCACCTGATGCTGTTACAGCGTATAATGGTTATCTTACTTCTTCTTCTAAAACACCTGAAG +AACATTTTATTGAAACCATCTCACTTGCTGGTTCCTATAAAGATTGGTCCTATTCTGGACAATCTACACA +ACTAGGTATAGAATTTCTTAAGAGAGGTGATAAAAGTGTATATTACACTAGTAATCCTACCACATTCCAC +CTAGATGGTGAAGTTATCACCTTTGACAATCTTAAGACACTTCTTTCTTTGAGAGAAGTGAGGACTATTA +AGGTGTTTACAACAGTAGACAACATTAACCTCCACACGCAAGTTGTGGACATGTCAATGACATATGGACA +ACAGTTTGGTCCAACTTATTTGGATGGAGCTGATGTTACTAAAATAAAACCTCATAATTCACATGAAGGT +AAAACATTTTATGTTTTACCTAATGATGACACTCTACGTGTTGAGGCTTTTGAGTACTACCACACAACTG +ATCCTAGTTTTCTGGGTAGGTACATGTCAGCATTAAATCACACTAAAAAGTGGAAATACCCACAAGTTAA +TGGTTTAACTTCTATTAAATGGGCAGATAACAACTGTTATCTTGCCACTGCATTGTTAACACTCCAACAA +ATAGAGTTGAAGTTTAATCCACCTGCTCTACAAGATGCTTATTACAGAGCAAGGGCTGGTGAAGCTGCTA +ACTTTTGTGCACTTATCTTAGCCTACTGTAATAAGACAGTAGGTGAGTTAGGTGATGTTAGAGAAACAAT +GAGTTACTTGTTTCAACATGCCAATTTAGATTCTTGCAAAAGAGTCTTGAACGTGGTGTGTAAAACTTGT +GGACAACAGCAGACAACCCTTAAGGGTGTAGAAGCTGTTATGTACATGGGCACACTTTCTTATGAACAAT +TTAAGAAAGGTGTTCAGATACCTTGTACGTGTGGTAAACAAGCTACAAAATATCTAGTACAACAGGAGTC +ACCTTTTGTTATGATGTCAGCACCACCTGCTCAGTATGAACTTAAGCATGGTACATTTACTTGTGCTAGT +GAGTACACTGGTAATTACCAGTGTGGTCACTATAAACATATAACTTCTAAAGAAACTTTGTATTGCATAG +ACGGTGCTTTACTTACAAAGTCCTCAGAATACAAAGGTCCTATTACGGATGTTTTCTACAAAGAAAACAG +TTACACAACAACCATAAAACCAGTTACTTATAAATTGGATGGTGTTGTTTGTACAGAAATTGACCCTAAG +TTGGACAATTATTATAAGAAAGACAATTCTTATTTCACAGAGCAACCAATTGATCTTGTACCAAACCAAC +CATATCCAAACGCAAGCTTCGATAATTTTAAGTTTGTATGTGATAATATCAAATTTGCTGATGATTTAAA +CCAGTTAACTGGTTATAAGAAACCTGCTTCAAGAGAGCTTAAAGTTACATTTTTCCCTGACTTAAATGGT +GATGTGGTGGCTATTGATTATAAACACTACACACCCTCTTTTAAGAAAGGAGCTAAATTGTTACATAAAC +CTATTGTTTGGCATGTTAACAATGCAACTAATAAAGCCACGTATAAACCAAATACCTGGTGTATACGTTG +TCTTTGGAGCACAAAACCAGTTGAAACATCAAATTCGTTTGATGTACTGAAGTCAGAGGACGCGCAGGGA +ATGGATAATCTTGCCTGCGAAGATCTAAAACCAGTCTCTGAAGAAGTAGTGGAAAATCCTACCATACAGA +AAGACGTTCTTGAGTGTAATGTGAAAACTACCGAAGTTGTAGGAGACATTATACTTAAACCAGCAAATAA +TAGTTTAAAAATTACAGAAGAGGTTGGCCACACAGATCTAATGGCTGCTTATGTAGACAATTCTAGTCTT +ACTATTAAGAAACCTAATGAATTATCTAGAGTATTAGGTTTGAAAACCCTTGCTACTCATGGTTTAGCTG +CTGTTAATAGTGTCCCTTGGGATACTATAGCTAATTATGCTAAGCCTTTTCTTAACAAAGTTGTTAGTAC +AACTACTAACATAGTTACACGGTGTTTAAACCGTGTTTGTACTAATTATATGCCTTATTTCTTTACTTTA +TTGCTACAATTGTGTACTTTTACTAGAAGTACAAATTCTAGAATTAAAGCATCTATGCCGACTACTATAG +CAAAGAATACTGTTAAGAGTGTCGGTAAATTTTGTCTAGAGGCTTCATTTAATTATTTGAAGTCACCTAA +TTTTTCTAAACTGATAAATATTATAATTTGGTTTTTACTATTAAGTGTTTGCCTAGGTTCTTTAATCTAC +TCAACCGCTGCTTTAGGTGTTTTAATGTCTAATTTAGGCATGCCTTCTTACTGTACTGGTTACAGAGAAG +GCTATTTGAACTCTACTAATGTCACTATTGCAACCTACTGTACTGGTTCTATACCTTGTAGTGTTTGTCT +TAGTGGTTTAGATTCTTTAGACACCTATCCTTCTTTAGAAACTATACAAATTACCATTTCATCTTTTAAA +TGGGATTTAACTGCTTTTGGCTTAGTTGCAGAGTGGTTTTTGGCATATATTCTTTTCACTAGGTTTTTCT +ATGTACTTGGATTGGCTGCAATCATGCAATTGTTTTTCAGCTATTTTGCAGTACATTTTATTAGTAATTC +TTGGCTTATGTGGTTAATAATTAATCTTGTACAAATGGCCCCGATTTCAGCTATGGTTAGAATGTACATC +TTCTTTGCATCATTTTATTATGTATGGAAAAGTTATGTGCATGTTGTAGACGGTTGTAATTCATCAACTT +GTATGATGTGTTACAAACGTAATAGAGCAACAAGAGTCGAATGTACAACTATTGTTAATGGTGTTAGAAG +GTCCTTTTATGTCTATGCTAATGGAGGTAAAGGCTTTTGCAAACTACACAATTGGAATTGTGTTAATTGT +GATACATTCTGTGCTGGTAGTACATTTATTAGTGATGAAGTTGCGAGAGACTTGTCACTACAGTTTAAAA +GACCAATAAATCCTACTGACCAGTCTTCTTACATCGTTGATAGTGTTACAGTGAAGAATGGTTCCATCCA +TCTTTACTTTGATAAAGCTGGTCAAAAGACTTATGAAAGACATTCTCTCTCTCATTTTGTTAACTTAGAC +AACCTGAGAGCTAATAACACTAAAGGTTCATTGCCTATTAATGTTATAGTTTTTGATGGTAAATCAAAAT +GTGAAGAATCATCTGCAAAATCAGCGTCTGTTTACTACAGTCAGCTTATGTGTCAACCTATACTGTTACT +AGATCAGGCATTAGTGTCTGATGTTGGTGATAGTGCGGAAGTTGCAGTTAAAATGTTTGATGCTTACGTT +AATACGTTTTCATCAACTTTTAACGTACCAATGGAAAAACTCAAAACACTAGTTGCAACTGCAGAAGCTG +AACTTGCAAAGAATGTGTCCTTAGACAATGTCTTATCTACTTTTATTTCAGCAGCTCGGCAAGGGTTTGT +TGATTCAGATGTAGAAACTAAAGATGTTGTTGAATGTCTTAAATTGTCACATCAATCTGACATAGAAGTT +ACTGGCGATAGTTGTAATAACTATATGCTCACCTATAACAAAGTTGAAAACATGACACCCCGTGACCTTG +GTGCTTGTATTGACTGTAGTGCGCGTCATATTAATGCGCAGGTAGCAAAAAGTCACAACATTGCTTTGAT +ATGGAACGTTAAAGATTTCATGTCATTGTCTGAACAACTACGAAAACAAATACGTAGTGCTGCTAAAAAG +AATAACTTACCTTTTAAGTTGACATGTGCAACTACTAGACAAGTTGTTAATGTTGTAACAACAAAGATAG +CACTTAAGGGTGGTAAAATTGTTAATAATTGGTTGAAGCAGTTAATTAAAGTTACACTTGTGTTCCTTTT +TGTTGCTGCTATTTTCTATTTAATAACACCTGTTCATGTCATGTCTAAACATACTGACTTTTCAAGTGAA +ATCATAGGATACAAGGCTATTGATGGTGGTGTCACTCGTGACATAGCATCTACAGATACTTGTTTTGCTA +ACAAACATGCTGATTTTGACACATGGTTTAGCCAGCGTGGTGGTAGTTATACTAATGACAAAGCTTGCCC +ATTGATTGCTGCAGTCATAACAAGAGAAGTGGGTTTTGTCGTGCCTGGTTTGCCTGGCACGATATTACGC +ACAACTAATGGTGACTTTTTGCATTTCTTACCTAGAGTTTTTAGTGCAGTTGGTAACATCTGTTACACAC +CATCAAAACTTATAGAGTACACTGACTTTGCAACATCAGCTTGTGTTTTGGCTGCTGAATGTACAATTTT +TAAAGATGCTTCTGGTAAGCCAGTACCATATTGTTATGATACCAATGTACTAGAAGGTTCTGTTGCTTAT +GAAAGTTTACGCCCTGACACACGTTATGTGCTCATGGATGGCTCTATTATTCAATTTCCTAACACCTACC +TTGAAGGTTCTGTTAGAGTGGTAACAACTTTTGATTCTGAGTACTGTAGGCACGGCACTTGTGAAAGATC +AGAAGCTGGTGTTTGTGTATCTACTAGTGGTAGATGGGTACTTAACAATGATTATTACAGATCTTTACCA +GGAGTTTTCTGTGGTGTAGATGCTGTAAATTTACTTACTAATATGTTTACACCACTAATTCAACCTATTG +GTGCTTTGGACATATCAGCATCTATAGTAGCTGGTGGTATTGTAGCTATCGTAGTAACATGCCTTGCCTA +CTATTTTATGAGGTTTAGAAGAGCTTTTGGTGAATACAGTCATGTAGTTGCCTTTAATACTTTACTATTC +CTTATGTCATTCACTGTACTCTGTTTAACACCAGTTTACTCATTCTTACCTGGTGTTTATTCTGTTATTT +ACTTGTACTTGACATTTTATCTTACTAATGATGTTTCTTTTTTAGCACATATTCAGTGGATGGTTATGTT +CACACCTTTAGTACCTTTCTGGATAACAATTGCTTATATCATTTGTATTTCCACAAAGCATTTCTATTGG +TTCTTTAGTAATTACCTAAAGAGACGTGTAGTCTTTAATGGTGTTTCCTTTAGTACTTTTGAAGAAGCTG +CGCTGTGCACCTTTTTGTTAAATAAAGAAATGTATCTAAAGTTGCGTAGTGATGTGCTATTACCTCTTAC +GCAATATAATAGATACTTAGCTCTTTATAATAAGTACAAGTATTTTAGTGGAGCAATGGATACAACTAGC +TACAGAGAAGCTGCTTGTTGTCATCTCGCAAAGGCTCTCAATGACTTCAGTAACTCAGGTTCTGATGTTC +TTTACCAACCACCACAAACCTCTATCACCTCAGCTGTTTTGCAGAGTGGTTTTAGAAAAATGGCATTCCC +ATCTGGTAAAGTTGAGGGTTGTATGGTACAAGTAACTTGTGGTACAACTACACTTAACGGTCTTTGGCTT +GATGACGTAGTTTACTGTCCAAGACATGTGATCTGCACCTCTGAAGACATGCTTAACCCTAATTATGAAG +ATTTACTCATTCGTAAGTCTAATCATAATTTCTTGGTACAGGCTGGTAATGTTCAACTCAGGGTTATTGG +ACATTCTATGCAAAATTGTGTACTTAAGCTTAAGGTTGATACAGCCAATCCTAAGACACCTAAGTATAAG +TTTGTTCGCATTCAACCAGGACAGACTTTTTCAGTGTTAGCTTGTTACAATGGTTCACCATCTGGTGTTT +ACCAATGTGCTATGAGGCCCAATTTCACTATTAAGGGTTCATTCCTTAATGGTTCATGTGGTAGTGTTGG +TTTTAACATAGATTATGACTGTGTCTCTTTTTGTTACATGCACCATATGGAATTACCAACTGGAGTTCAT +GCTGGCACAGACTTAGAAGGTAACTTTTATGGACCTTTTGTTGACAGGCAAACAGCACAAGCAGCTGGTA +CGGACACAACTATTACAGTTAATGTTTTAGCTTGGTTGTACGCTGCTGTTATAAATGGAGACAGGTGGTT +TCTCAATCGATTTACCACAACTCTTAATGACTTTAACCTTGTGGCTATGAAGTACAATTATGAACCTCTA +ACACAAGACCATGTTGACATACTAGGACCTCTTTCTGCTCAAACTGGAATTGCCGTTTTAGATATGTGTG +CTTCATTAAAAGAATTACTGCAAAATGGTATGAATGGACGTACCATATTGGGTAGTGCTTTATTAGAAGA +TGAATTTACACCTTTTGATGTTGTTAGACAATGCTCAGGTGTTACTTTCCAAAGTGCAGTGAAAAGAACA +ATCAAGGGTACACACCACTGGTTGTTACTCACAATTTTGACTTCACTTTTAGTTTTAGTCCAGAGTACTC +AATGGTCTTTGTTCTTTTTTTTGTATGAAAATGCCTTTTTACCTTTTGCTATGGGTATTATTGCTATGTC +TGCTTTTGCAATGATGTTTGTCAAACATAAGCATGCATTTCTCTGTTTGTTTTTGTTACCTTCTCTTGCC +ACTGTAGCTTATTTTAATATGGTCTATATGCCTGCTAGTTGGGTGATGCGTATTATGACATGGTTGGATA +TGGTTGATACTAGTTTGTCTGGTTTTAAGCTAAAAGACTGTGTTATGTATGCATCAGCTGTAGTGTTACT +AATCCTTATGACAGCAAGAACTGTGTATGATGATGGTGCTAGGAGAGTGTGGACACTTATGAATGTCTTG +ACACTCGTTTATAAAGTTTATTATGGTAATGCTTTAGATCAAGCCATTTCCATGTGGGCTCTTATAATCT +CTGTTACTTCTAACTACTCAGGTGTAGTTACAACTGTCATGTTTTTGGCCAGAGGTATTGTTTTTATGTG +TGTTGAGTATTGCCCTATTTTCTTCATAACTGGTAATACACTTCAGTGTATAATGCTAGTTTATTGTTTC +TTAGGCTATTTTTGTACTTGTTACTTTGGCCTCTTTTGTTTACTCAACCGCTACTTTAGACTGACTCTTG +GTGTTTATGATTACTTAGTTTCTACACAGGAGTTTAGATATATGAATTCACAGGGACTACTCCCACCCAA +GAATAGCATAGATGCCTTCAAACTCAACATTAAATTGTTGGGTGTTGGTGGCAAACCTTGTATCAAAGTA +GCCACTGTACAGTCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAAC +TCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAA +AGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTA +GACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAAGCTATAGCCTCAGAGTTTA +GTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGA +TTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCA +GCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTG +AGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAA +TGATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACA +ACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACAT +TTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAG +TGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCT +GCTGTCAAATTACAGAATAATGAGCTTAGTCCTGTTGCACTACGACAGATGTCTTGTGCTGCCGGTACTA +CACAAACTGCTTGCACTGATGACAATGCGTTAGCTTACTACAACACAACAAAGGGAGGTAGGTTTGTACT +TGCACTGTTATCCGATTTACAGGATTTGAAATGGGCTAGATTCCCTAAGAGTGATGGAACTGGTACTATC +TATACAGAACTGGAACCACCTTGTAGGTTTGTTACAGACACACCTAAAGGTCCTAAAGTGAAGTATTTAT +ACTTTATTAAAGGATTAAACAACCTAAATAGAGGTATGGTACTTGGTAGTTTAGCTGCCACAGTACGTCT +ACAAGCTGGTAATGCAACAGAAGTGCCTGCCAATTCAACTGTATTATCTTTCTGTGCTTTTGCTGTAGAT +GCTGCTAAAGCTTACAAAGATTATCTAGCTAGTGGGGGACAACCAATCACTAATTGTGTTAAGATGTTGT +GTACACACACTGGTACTGGTCAGGCAATAACAGTTACACCGGAAGCCAATATGGATCAAGAATCCTTTGG +TGGTGCATCGTGTTGTCTGTACTGCCGTTGCCACATAGATCATCCAAATCCTAAAGGATTTTGTGACTTA +AAAGGTAAGTATGTACAAATACCTACAACTTGTGCTAATGACCCTGTGGGTTTTACACTTAAAAACACAG +TCTGTACCGTCTGCGGTATGTGGAAAGGTTATGGCTGTAGTTGTGATCAACTCCGCGAACCCATGCTTCA +GTCAGCTGATGCACAATCGTTTTTAAACGGGTTTGCGGTGTAAGTGCAGCCCGTCTTACACCGTGCGGCA +CAGGCACTAGTACTGATGTCGTATACAGGGCTTTTGACATCTACAATGATAAAGTAGCTGGTTTTGCTAA +ATTCCTAAAAACTAATTGTTGTCGCTTCCAAGAAAAGGACGAAGATGACAATTTAATTGATTCTTACTTT +GTAGTTAAGAGACACACTTTCTCTAACTACCAACATGAAGAAACAATTTATAATTTACTTAAGGATTGTC +CAGCTGTTGCTAAACATGACTTCTTTAAGTTTAGAATAGACGGTGACATGGTACCACATATATCACGTCA +ACGTCTTACTAAATACACAATGGCAGACCTCGTCTATGCTTTAAGGCATTTTGATGAAGGTAATTGTGAC +ACATTAAAAGAAATACTTGTCACATACAATTGTTGTGATGATGATTATTTCAATAAAAAGGACTGGTATG +ATTTTGTAGAAAACCCAGATATATTACGCGTATACGCCAACTTAGGTGAACGTGTACGCCAAGCTTTGTT +AAAAACAGTACAATTCTGTGATGCCATGCGAAATGCTGGTATTGTTGGTGTACTGACATTAGATAATCAA +GATCTCAATGGTAACTGGTATGATTTCGGTGATTTCATACAAACCACGCCAGGTAGTGGAGTTCCTGTTG +TAGATTCTTATTATTCATTGTTAATGCCTATATTAACCTTGACCAGGGCTTTAACTGCAGAGTCACATGT +TGACACTGACTTAACAAAGCCTTACATTAAGTGGGATTTGTTAAAATATGACTTCACGGAAGAGAGGTTA +AAACTCTTTGACCGTTATTTTAAATATTGGGATCAGACATACCACCCAAATTGTGTTAACTGTTTGGATG +ACAGATGCATTCTGCATTGTGCAAACTTTAATGTTTTATTCTCTACAGTGTTCCCACCTACAAGTTTTGG +ACCACTAGTGAGAAAAATATTTGTTGATGGTGTTCCATTTGTAGTTTCAACTGGATACCACTTCAGAGAG +CTAGGTGTTGTACATAATCAGGATGTAAACTTACATAGCTCTAGACTTAGTTTTAAGGAATTACTTGTGT +ATGCTGCTGACCCTGCTATGCACGCTGCTTCTGGTAATCTATTACTAGATAAACGCACTACGTGCTTTTC +AGTAGCTGCACTTACTAACAATGTTGCTTTTCAAACTGTCAAACCCGGTAATTTTAACAAAGACTTCTAT +GACTTTGCTGTGTCTAAGGGTTTCTTTAAGGAAGGAAGTTCTGTTGAATTAAAACACTTCTTCTTTGCTC +AGGATGGTAATGCTGCTATCAGCGATTATGACTACTATCGTTATAATCTACCAACAATGTGTGATATCAG +ACAACTACTATTTGTAGTTGAAGTTGTTGATAAGTACTTTGATTGTTACGATGGTGGCTGTATTAATGCT +AACCAAGTCATCGTCAACAACCTAGACAAATCAGCTGGTTTTCCATTTAATAAATGGGGTAAGGCTAGAC +TTTATTATGATTCAATGAGTTATGAGGATCAAGATGCACTTTTCGCATATACAAAACGTAATGTCATCCC +TACTATAACTCAAATGAATCTTAAGTATGCCATTAGTGCAAAGAATAGAGCTCGCACCGTAGCTGGTGTC +TCTATCTGTAGTACTATGACCAATAGACAGTTTCATCAAAAATTATTGAAATCAATAGCCGCCACTAGAG +GAGCTACTGTAGTAATTGGAACAAGCAAATTCTATGGTGGTTGGCACAACATGTTAAAAACTGTTTATAG +TGATGTAGAAAACCCTCACCTTATGGGTTGGGATTATCCTAAATGTGATAGAGCCATGCCTAACATGCTT +AGAATTATGGCCTCACTTGTTCTTGCTCGCAAACATACAACGTGTTGTAGCTTGTCACACCGTTTCTATA +GATTAGCTAATGAGTGTGCTCAAGTATTGAGTGAAATGGTCATGTGTGGCGGTTCACTATATGTTAAACC +AGGTGGAACCTCATCAGGAGATGCCACAACTGCTTATGCTAATAGTGTTTTTAACATTTGTCAAGCTGTC +ACGGCCAATGTTAATGCACTTTTATCTACTGATGGTAACAAAATTGCCGATAAGTATGTCCGCAATTTAC +AACACAGACTTTATGAGTGTCTCTATAGAAATAGAGATGTTGACACAGACTTTGTGAATGAGTTTTACGC +ATATTTGCGTAAACATTTCTCAATGATGATACTCTCTGACGATGCTGTTGTGTGTTTCAATAGCACTTAT +GCATCTCAAGGTCTAGTGGCTAGCATAAAGAACTTTAAGTCAGTTCTTTATTATCAAAACAATGTTTTTA +TGTCTGAAGCAAAATGTTGGACTGAGACTGACCTTACTAAAGGACCTCATGAATTTTGCTCTCAACATAC +AATGCTAGTTAAACAGGGTGATGATTATGTGTACCTTCCTTACCCAGATCCATCAAGAATCCTAGGGGCC +GGCTGTTTTGTAGATGATATCGTAAAAACAGATGGTACACTTATGATTGAACGGTTCGTGTCTTTAGCTA +TAGATGCTTACCCACTTACTAAACATCCTAATCAGGAGTATGCTGATGTCTTTCATTTGTACTTACAATA +CATAAGAAAGCTACATGATGAGTTAACAGGACACATGTTAGACATGTATTCTGTTATGCTTACTAATGAT +AACACTTCAAGGTATTGGGAACCTGAGTTTTATGAGGCTATGTACACACCGCATACAGTCTTACAGGCTG +TTGGGGCTTGTGTTCTTTGCAATTCACAGACTTCATTAAGATGTGGTGCTTGCATACGTAGACCATTCTT +ATGTTGTAAATGCTGTTACGACCATGTCATATCAACATCACATAAATTAGTCTTGTCTGTTAATCCGTAT +GTTTGCAATGCTCCAGGTTGTGATGTCACAGATGTGACTCAACTTTACTTAGGAGGTATGAGCTATTATT +GTAAATCACATAAACCACCCATTAGTTTTCCATTGTGTGCTAATGGACAAGTTTTTGGTTTATATAAAAA +TACATGTGTTGGTAGCGATAATGTTACTGACTTTAATGCAATTGCAACATGTGACTGGACAAATGCTGGT +GATTACATTTTAGCTAACACCTGTACTGAAAGACTCAAGCTTTTTGCAGCAGAAACGCTCAAAGCTACTG +AGGAGACATTTAAACTGTCTTATGGTATTGCTACTGTACGTGAAGTGCTGTCTGACAGAGAATTACATCT +TTCATGGGAAGTTGGTAAACCTAGACCACCACTTAACCGAAATTATGTCTTTACTGGTTATCGTGTAACT +AAAAACAGTAAAGTACAAATAGGAGAGTACACCTTTGAAAAAGGTGACTATGGTGATGCTGTTGTTTACC +GAGGTACAACAACTTACAAATTAAATGTTGGTGATTATTTTGTGCTGACATCACATACAGTAATGCCATT +AAGTGCACCTACACTAGTGCCACAAGAGCACTATGTTAGAATTACTGGCTTATACCCAACACTCAATATC +TCAGATGAGTTTTCTAGCAATGTTGCAAATTATCAAAAGGTTGGTATGCAAAAGTATTCTACACTCCAGG +GACCACCTGGTACTGGTAAGAGTCATTTTGCTATTGGCCTAGCTCTCTACTACCCTTCTGCTCGCATAGT +GTATACAGCTTGCTCTCATGCCGCTGTTGATGCACTATGTGAGAAGGCATTAAAATATTTGCCTATAGAT +AAATGTAGTAGAATTATACCTGCACGTGCTCGTGTAGAGTGTTTTGATAAATTCAAAGTGAATTCAACAT +TAGAACAGTATGTCTTTTGTACTGTAAATGCATTGCCTGAGACGACAGCAGATATAGTTGTCTTTGATGA +AATTTCAATGGCCACAAATTATGATTTGAGTGTTGTCAATGCCAGATTACGTGCTAAGCACTATGTGTAC +ATTGGCGACCCTGCTCAATTACCTGCACCACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATT +TCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCC +TGCTGAAATTGTTGACACTGTGAGTGCTTTGGTTTATGATAATAAGCTTAAAGCACATAAAGACAAATCA +GCTCAATGCTTTAAAATGTTTTATAAGGGTGTTATCACGCATGATGTTTCATCTGCAATTAACAGGCCAC +AAATAGGCGTGGTAAGAGAATTCCTTACACGTAACCCTGCTTGGAGAAAAGCTGTCTTTATTTCACCTTA +TAATTCACAGAATGCTGTAGCCTCAAAGATTTTGGGACTACCAACTCAAACTGTTGATTCATCACAGGGC +TCAGAATATGACTATGTCATATTCACTCAAACCACTGAAACAGCTCACTCTTGTAATGTAAACAGATTTA +ATGTTGCTATTACCAGAGCAAAAGTAGGCATACTTTGCATAATGTCTGATAGAGACCTTTATGACAAGTT +GCAATTTACAAGTCTTGAAATTCCACGTAGGAATGTGGCAACTTTACAAGCTGAAAATGTAACAGGACTC +TTTAAAGATTGTAGTAAGGTAATCACTGGGTTACATCCTACACAGGCACCTACACACCTCAGTGTTGACA +CTAAATTCAAAACTGAAGGTTTATGTGTTGACATACCTGGCATACCTAAGGACATGACCTATAGAAGACT +CATCTCTATGATGGGTTTTAAAATGAATTATCAAGTTAATGGTTACCCTAACATGTTTATCACCCGCGAA +GAAGCTATAAGACATGTACGTGCATGGATTGGCTTCGATGTCGAGGGGTGTCATGCTACTAGAGAAGCTG +TTGGTACCAATTTACCTTTACAGCTAGGTTTTTCTACAGGTGTTAACCTAGTTGCTGTACCTACAGGTTA +TGTTGATACACCTAATAATACAGATTTTTCCAGAGTTAGTGCTAAACCACCGCCTGGAGATCAATTTAAA +CACCTCATACCACTTATGTACAAAGGACTTCCTTGGAATGTAGTGCGTATAAAGATTGTACAAATGTTAA +GTGACACACTTAAAAATCTCTCTGACAGAGTCGTATTTGTCTTATGGGCACATGGCTTTGAGTTGACATC +TATGAAGTATTTTGTGAAAATAGGACCTGAGCGCACCTGTTGTCTATGTGATAGACGTGCCACATGCTTT +TCCACTGCTTCAGACACTTATGCCTGTTGGCATCATTCTATTGGATTTGATTACGTCTATAATCCGTTTA +TGATTGATGTTCAACAATGGGGTTTTACAGGTAACCTACAAAGCAACCATGATCTGTATTGTCAAGTCCA +TGGTAATGCACATGTAGCTAGTTGTGATGCAATCATGACTAGGTGTCTAGCTGTCCACGAGTGCTTTGTT +AAGCGTGTTGACTGGACTATTGAATATCCTATAATTGGTGATGAACTGAAGATTAATGCGGCTTGTAGAA +AGGTTCAACACATGGTTGTTAAAGCTGCATTATTAGCAGACAAATTCCCAGTTCTTCACGACATTGGTAA +CCCTAAAGCTATTAAGTGTGTACCTCAAGCTGATGTAGAATGGAAGTTCTATGATGCACAGCCTTGTAGT +GACAAAGCTTATAAAATAGAAGAATTATTCTATTCTTATGCCACACATTCTGACAAATTCACAGATGGTG +TATGCCTATTTTGGAATTGCAATGTCGATAGATATCCTGCTAATTCCATTGTTTGTAGATTTGACACTAG +AGTGCTATCTAACCTTAACTTGCCTGGTTGTGATGGTGGCAGTTTGTATGTAAATAAACATGCATTCCAC +ACACCAGCTTTTGATAAAAGTGCTTTTGTTAATTTAAAACAATTACCATTTTTCTATTACTCTGACAGTC +CATGTGAGTCTCATGGAAAACAAGTAGTGTCAGATATAGATTATGTACCACTAAAGTCTGCTACGTGTAT +AACACGTTGCAATTTAGGTGGTGCTGTCTGTAGACATCATGCTAATGAGTACAGATTGTATCTCGATGCT +TATAACATGATGATCTCAGCTGGCTTTAGCTTGTGGGTTTACAAACAATTTGATACTTATAACCTCTGGA +ACACTTTTACAAGACTTCAGAGTTTAGAAAATGTGGCTTTTAATGTTGTAAATAAGGGACACTTTGATGG +ACAACAGGGTGAAGTACCAGTTTCTATCATTAATAACACTGTTTACACAAAAGTTGATGGTGTTGATGTA +GAATTGTTTGAAAATAAAACAACATTACCTGTTAATGTAGCATTTGAGCTTTGGGCTAAGCGCAACATTA +AACCAGTACCAGAGGTGAAAATACTCAATAATTTGGGTGTGGACATTGCTGCTAATACTGTGATCTGGGA +CTACAAAAGAGATGCTCCAGCACATATATCTACTATTGGTGTTTGTTCTATGACTGACATAGCCAAGAAA +CCAACTGAAACGATTTGTGCACCACTCACTGTCTTTTTTGATGGTAGAGTTGATGGTCAAGTAGACTTAT +TTAGAAATGCCCGTAATGGTGTTCTTATTACAGAAGGTAGTGTTAAAGGTTTACAACCATCTGTAGGTCC +CAAACAAGCTAGTCTTAATGGAGTCACATTAATTGGAGAAGCCGTAAAAACACAGTTCAATTATTATAAG +AAAGTTGATGGTGTTGTCCAACAATTACCTGAAACTTACTTTACTCAGAGTAGAAATTTACAAGAATTTA +AACCCAGGAGTCAAATGGAAATTGATTTCTTAGAATTAGCTATGGATGAATTCATTGAACGGTATAAATT +AGAAGGCTATGCCTTCGAACATATCGTTTATGGAGATTTTAGTCATAGTCAGTTAGGTGGTTTACATCTA +CTGATTGGACTAGCTAAACGTTTTAAGGAATCACCTTTTGAATTAGAAGATTTTATTCCTATGGACAGTA +CAGTTAAAAACTATTTCATAACAGATGCGCAAACAGGTTCATCTAAGTGTGTGTGTTCTGTTATTGATTT +ATTACTTGATGATTTTGTTGAAATAATAAAATCCCAAGATTTATCTGTAGTTTCTAAGGTTGTCAAAGTG +ACTATTGACTATACAGAAATTTCATTTATGCTTTGGTGTAAAGATGGCCATGTAGAAACATTTTACCCAA +AATTACAATCTAGTCAAGCGTGGCAACCGGGTGTTGCTATGCCTAATCTTTACAAAATGCAAAGAATGCT +ATTAGAAAAGTGTGACCTTCAAAATTATGGTGATAGTGCAACATTACCTAAAGGCATAATGATGAATGTC +GCAAAATATACTCAACTGTGTCAATATTTAAACACATTAACATTAGCTGTACCCTATAATATGAGAGTTA +TACATTTTGGTGCTGGTTCTGATAAAGGAGTTGCACCAGGTACAGCTGTTTTAAGACAGTGGTTGCCTAC +GGGTACGCTGCTTGTCGATTCAGATCTTAATGACTTTGTCTCTGATGCAGATTCAACTTTGATTGGTGAT +TGTGCAACTGTACATACAGCTAATAAATGGGATCTCATTATTAGTGATATGTACGACCCTAAGACTAAAA +ATGTTACAAAAGAAAATGACTCTAAAGAGGGTTTTTTCACTTACATTTGTGGGTTTATACAACAAAAGCT +AGCTCTTGGAGGTTCCGTGGCTATAAAGATAACAGAACATTCTTGGAATGCTGATCTTTATAAGCTCATG +GGACACTTCGCATGGTGGACAGCCTTTGTTACTAATGTGAATGCGTCATCATCTGAAGCATTTTTAATTG +GATGTAATTATCTTGGCAAACCACGCGAACAAATAGATGGTTATGTCATGCATGCAAATTACATATTTTG +GAGGAATACAAATCCAATTCAGTTGTCTTCCTATTCTTTATTTGACATGAGTAAATTTCCCCTTAAATTA +AGGGGTACTGCTGTTATGTCTTTAAAAGAAGGTCAAATCAATGATATGATTTTATCTCTTCTTAGTAAAG +GTAGACTTATAATTAGAGAAAACAACAGAGTTGTTATTTCTAGTGATGTTCTTGTTAACAACTAAACGAA +CAATGTTTGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACCAGAACTCA +ATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGACAAAGTTTTCAGATCCTCA +GTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCCAATGTTACTTGGTTCCATGCTATACATG +TCTCTGGGACCAATGGTACTAAGAGGTTTGATAACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGC +TTCCACTGAGAAGTCTAACATAATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCC +CTACTTATTGTTAATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATGATCCAT +TTTTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTATTCTAGTGC +GAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAAGGAAAACAGGGTAATTTC +AAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTATTTTAAAATATATTCTAAGCACACGCCTA +TTAATTTAGTGCGTGATCTCCCTCAGGGTTTTTCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTAT +TAACATCACTAGGTTTCAAACTTTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCA +GGTTGGACAGCTGGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATA +ATGAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAGTGTACGTT +GAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTCCAACCAACAGAATCTATT +GTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAAGTTTTTAACGCCACCAGATTTGCATCTG +TTTATGCTTGGAACAGGAAGAGAATCAGCAACTGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATC +ATTTTCCACTTTTAAGTGTTATGGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTAT +GCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTG +ATTATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAATCTTGATTC +TAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAATCTCAAACCTTTTGAGAGA +GATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGTAATGGTGTTGAAGGTTTTAATTGTTACT +TTCCTTTACAATCATATGGTTTCCAACCCACTAATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACT +TTCTTTTGAACTTCTACATGCACCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAAC +AAATGTGTCAATTTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTC +TGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAGACACTTGA +GATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCAGGAACAAATACTTCTAAC +CAGGTTGCTGTTCTTTATCAGGATGTTAACTGCACAGAAGTCCCTGTTGCTATTCATGCAGATCAACTTA +CTCCTACTTGGCGTGTTTATTCTACAGGTTCTAATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGC +TGAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACT +CAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTG +GTGCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATTAGTGTTAC +CACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATGTACATTTGTGGTGATTCA +ACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGTACACAATTAAACCGTGCTTTAACTGGAA +TAGCTGTTGAACAAGACAAAAACACCCAAGAAGTTTTTGCACAAGTCAAACAAATTTACAAAACACCACC +AATTAAAGATTTTGGTGGTTTTAATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCA +TTTATTGAAGATCTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATT +GCCTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTTTTGCCACC +TTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGTACAATCACTTCTGGTTGG +ACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATGCAAATGGCTTATAGGTTTAATGGTATTG +GAGTTACACAGAATGTTCTCTATGAGAACCAAAAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAA +AATTCAAGACTCACTTTCTTCCACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCA +CAAGCTTTAAACACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATA +TCCTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGACTTCAAAG +TTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCTTCTGCTAATCTTGCTGCT +ACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTTGATTTTTGTGGAAAGGGCTATCATCTTA +TGTCCTTCCCTCAGTCAGCACCTCATGGTGTAGTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAA +GAACTTCACAACTGCTCCTGCCATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTT +TCAAATGGCACACACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACA +CATTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCTTTGCAACC +TGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACATCACCAGATGTTGATTTA +GGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAAAAAGAAATTGACCGCCTCAATGAGGTTG +CCAAGAATTTAAATGAATCTCTCATCGATCTCCAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCC +ATGGTACATTTGGCTAGGTTTTATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGT +ATGACCAGTTGCTGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACG +ACTCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACATAAACGAACTTATGGATTTGTTTATGAGA +ATCTTCACAATTGGAACTGTAACTTTGAAGCAAGGTGAAATCAAGGATGCTACTCCTTCAGATTTTGTTC +GCGCTACTGCAACGATACCGATACAAGCCTCACTCCCTTTCGGATGGCTTATTGTTGGCGTTGCACTTCT +TGCTGTTTTTCAGAGCGCTTCCAAAATCATAACCCTCAAAAAGAGATGGCAACTAGCACTCTCCAAGGGT +GTTCACTTTGTTTGCAACTTGCTGTTGTTGTTTGTAACAGTTTACTCACACCTTTTGCTCGTTGCTGCTG +GCCTTGAAGCCCCTTTTCTCTATCTTTATGCTTTAGTCTACTTCTTGCAGAGTATAAACTTTGTAAGAAT +AATAATGAGGCTTTGGCTTTGCTGGAAATGCCGTTCCAAAAACCCATTACTTTATGATGCCAACTATTTT +CTTTGCTGGCATACTAATTGTTACGACTATTGTATACCTTACAATAGTGTAACTTCTTCAATTGTCATTA +CTTCAGGTGATGGCACAACAAGTCCTATTTCTGAACATGACTACCAGATTGGTGGTTATACTGAAAAATG +GGAATCTGGAGTAAAAGACTGTGTTGTATTACACAGTTACTTCACTTCAGACTATTACCAGCTGTACTCA +ACTCAATTGAGTACAGACACTGGTGTTGAACATGTTACCTTCTTCATCTACAATAAAATTGTTGATGAGC +CTGAAGAACATGTCCAAATTCACACAATCGACGGTTCATCCGGAGTTGTTAATCCAGTAATGGAACCAAT +TTATGATGAACCGACGACGACTACTAGCGTGCCTTTGTAAGCACAAGCTGATGAGTACGAACTTATGTAC +TCATTCGTTTCGGAAGAGACAGGTACGTTAATAGTTAATAGCGTACTTCTTTTTCTTGCTTTCGTGGTAT +TCTTGCTAGTTACACTAGCCATCCTTACTGCGCTTCGATTGTGTGCGTACTGCTGCAATATTGTTAACGT +GAGTCTTGTAAAACCTTCTTTTTACGTTTACTCTCGTGTTAAAAATCTGAATTCTTCTAGAGTTCCTGAT +CTTCTGGTCTAAACGAACTAAATATTATATTAGTTTTTCTGTTTGGAACTTTAATTTTAGCCATGGCAGA +TTCCAACGGTACTATTACCGTTGAAGAGCTTAAAAAGCTCCTTGAACAATGGAACCTAGTAATAGGTTTC +CTATTCCTTACATGGATTTGTCTTCTACAATTTGCCTATGCCAACAGGAATAGGTTTTTGTATATAATTA +AGTTAATTTTCCTCTGGCTGTTATGGCCAGTAACTTTAGCTTGTTTTGTGCTTGCTGCTGTTTACAGAAT +AAATTGGATCACCGGTGGAATTGCTATCGCAATGGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTC +ATTGCTTCTTTCAGACTGTTTGCGCGTACGCGTTCCATGTGGTCATTCAATCCAGAAACTAACATTCTTC +TCAACGTGCCACTCCATGGCACTATTCTGACCAGACCGCTTCTAGAAAGTGAACTCGTAATCGGAGCTGT +GATCCTTCGTGGACATCTTCGTATTGCTGGACACCATCTAGGACGCTGTGACATCAAGGACCTGCCTAAA +GAAATCACTGTTGCTACATCACGAACGCTTTCTTATTACAAATTGGGAGCTTCGCAGCGTGTAGCAGGTG +ACTCAGGTTTTGCTGCATACAGTCGCTACAGGATTGGCAACTATAAATTAAACACAGACCATTCCAGTAG +CAGTGACAATATTGCTTTGCTTGTACAGTAAGTGACAACAGATGTTTCATCTCGTTGACTTTCAGGTTAC +TATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATA +AACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAAC +CAATGGAGATTGATTAAACGAACATGAAAATTATTCTTTTCTTGGCACTGATAACACTCGCTACTTGTGA +GCTTTATCACTACCAAGAGTGTGTTAGAGGTACAACAGTACTTTTAAAAGAACCTTGCTCTTCTGGAACA +TACGAGGGCAATTCACCATTTCATCCTCTAGCTGATAACAAATTTGCACTGACTTGCTTTAGCACTCAAT +TTGCTTTTGCTTGTCCTGACGGCGTAAAACACGTCTATCAGTTACGTGCCAGATCAGTTTCACCTAAACT +GTTCATCAGACAAGAGGAAGTTCAAGAACTTTACTCTCCAATTTTTCTTATTGTTGCGGCAATAGTGTTT +ATAACACTTTGCTTCACACTCAAAAGAAAGACAGAATGATTGAACTTTCATTAATTGACTTCTATTTGTG +CTTTTTAGCCTTTCTGCTATTCCTTGTTTTAATTATGCTTATTATCTTTTGGTTCTCACTTGAACTGCAA +GATCATAATGAAACTTGTCACGCCTAAACGAACATGAAATTTCTTGTTTTCTTAGGAATCATCACAACTG +TAGCTGCATTTCACCAAGAATGTAGTTTACAGTCATGTACTCAACATCAACCATATGTAGTTGATGACCC +GTGTCCTATTCACTTCTATTCTAAATGGTATATTAGAGTAGGAGCTAGAAAATCAGCACCTTTAATTGAA +TTGTGCGTGGATGAGGCTGGTTCTAAATCACCCATTCAGTACATCGATATCGGTAATTATACAGTTTCCT +GTTTACCTTTTACAATTAATTGCCAGGAACCTAAATTGGGTAGTCTTGTAGTGCGTTGTTCGTTCTATGA +AGACTTTTTAGAGTATCATGACGTTCGTGTTGTTTTAGATTTCATCTAAACGAACAAACTAAAATGTCTG +ATAATGGACCCCAAAATCAGCGAAATGCACCCCGCATTACGTTTGGTGGACCCTCAGATTCAACTGGCAG +TAACCAGAATGGAGAACGCAGTGGGGCGCGATCAAAACAACGTCGGCCCCAAGGTTTACCCAATAATACT +GCGTCTTGGTTCACCGCTCTCACTCAACATGGCAAGGAAGACCTTAAATTCCCTCGAGGACAAGGCGTTC +CAATTAACACCAATAGCAGTCCAGATGACCAAATTGGCTACTACCGAAGAGCTACCAGACGAATTCGTGG +TGGTGACGGTAAAATGAAAGATCTCAGTCCAAGATGGTATTTCTACTACCTAGGAACTGGGCCAGAAGCT +GGACTTCCCTATGGTGCTAACAAAGACGGCATCATATGGGTTGCAACTGAGGGAGCCTTGAATACACCAA +AAGATCACATTGGCACCCGCAATCCTGCTAACAATGCTGCAATCGTGCTACAACTTCCTCAAGGAACAAC +ATTGCCAAAAGGCTTCTACGCAGAAGGGAGCAGAGGCGGCAGTCAAGCCTCTTCTCGTTCCTCATCACGT +AGTCGCAACAGTTCAAGAAATTCAACTCCAGGCAGCAGTAGGGGAACTTCTCCTGCTAGAATGGCTGGCA +ATGGCGGTGATGCTGCTCTTGCTTTGCTGCTGCTTGACAGATTGAACCAGCTTGAGAGCAAAATGTCTGG +TAAAGGCCAACAACAACAAGGCCAAACTGTCACTAAGAAATCTGCTGCTGAGGCTTCTAAGAAGCCTCGG +CAAAAACGTACTGCCACTAAAGCATACAATGTAACACAAGCTTTCGGCAGACGTGGTCCAGAACAAACCC +AAGGAAATTTTGGGGACCAGGAACTAATCAGACAAGGAACTGATTACAAACATTGGCCGCAAATTGCACA +ATTTGCCCCCAGCGCTTCAGCGTTCTTCGGAATGTCGCGCATTGGCATGGAAGTCACACCTTCGGGAACG +TGGTTGACCTACACAGGTGCCATCAAATTGGATGACAAAGATCCAAATTTCAAAGATCAAGTCATTTTGC +TGAATAAGCATATTGACGCATACAAAACATTCCCACCAACAGAGCCTAAAAAGGACAAAAAGAAGAAGGC +TGATGAAACTCAAGCCTTACCGCAGAGACAGAAGAAACAGCAAACTGTGACTCTTCTTCCTGCTGCAGAT +TTGGATGATTTCTCCAAACAATTGCAACAATCCATGAGCAGTGCTGACTCAACTCAGGCCTAAACTCATG +CAGACCACACAAGGCAGATGGGCTATATAAACGTTTTCGCTTTTCCGTTTACGATATATAGTCTACTCTT +GTGCAGAATGAATTCTCGTAACTACATAGCACAAGTAGATGTAGTTAACTTTAATCTCACATAGCAATCT +TTAATCAGTGTGTAACATTAGGGAGGACTTGAAAGAGCCACCACATTTTCACCGAGGCCACGCGGAGTAC +GATCGAGTGTACAGTGAACAATGCTAGGGAGAGCTGCCTATATGGAAGAGCCCTAATGTGTAAAATTAAT +TTTAGTAGTGCTATCCCCATGTGATTTTAATAGCTTCTTAGGAGAATGACAAAAAAAAAAAAAAAAAAAA +AAAAAAAAAAAAA diff --git a/test/data/broken/non-tiling/info.yml b/test/data/broken/non-tiling/info.yml new file mode 100644 index 0000000..133ad6c --- /dev/null +++ b/test/data/broken/non-tiling/info.yml @@ -0,0 +1,20 @@ +schema_version: 1.0.0-alpha +name: eden +amplicon_size: 2500 +version: v1 +organism: sars-cov-2 +aliases: +- sydney +developers: +- John-Sebastian Eden +- Eby Sim +definition_url: https://github.com/pha4ge/primer-schemes/tree/main/sars-cov-2/eden/v1 +citations: +- https://www.protocols.io/view/sars-cov-2-genome-sequencing-using-long-pooled-amp-kxygxeob4v8j/v1 +notes: +- Protocol includes addendum for ONT sequencing +license: CC-BY-4.0 +citations: + - https://dx.doi.org/10.17504/protocols.io.befyjbpw +primer_checksum: primaschema:55c9726eb1400cab +reference_checksum: primaschema:b1acd7163146bf17 diff --git a/test/data/broken/non-tiling/primer.bed b/test/data/broken/non-tiling/primer.bed new file mode 100644 index 0000000..67002ff --- /dev/null +++ b/test/data/broken/non-tiling/primer.bed @@ -0,0 +1,4 @@ +MN908947.3 31 55 SARS2_1_LEFT_1 1 + CCAACCAACTTTCGATCTCTTGTA +MN908947.3 2569 2593 SARS2_1_RIGHT_1 1 - AGCTTCAACAGCTTCACTAGTAGG +MN908947.3 3000 3022 SARS2_2_LEFT_1 2 + TCAGAGGCTGCTCGTGTTGTAC +MN908947.3 4000 4022 SARS2_2_RIGHT_1 2 - TAGTTTCCACACAGACAGGCAT diff --git a/test/data/broken/non-tiling/reference.fasta b/test/data/broken/non-tiling/reference.fasta new file mode 100644 index 0000000..e1cfd92 --- /dev/null +++ b/test/data/broken/non-tiling/reference.fasta @@ -0,0 +1,429 @@ +>MN908947.3 +ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAA +CGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAAC +TAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTG +TTGCAGCCGATCATCAGCACATCTAGGTTTCGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTC +CCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTAC +GTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGG +CTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAAACGTTCGGAT +GCTCGAACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACTCGAAGGCATTCAGTACGGTC +GTAGTGGTGAGACACTTGGTGTCCTTGTCCCTCATGTGGGCGAAATACCAGTGGCTTACCGCAAGGTTCT +TCTTCGTAAGAACGGTAATAAAGGAGCTGGTGGCCATAGTTACGGCGCCGATCTAAAGTCATTTGACTTA +GGCGACGAGCTTGGCACTGATCCTTATGAAGATTTTCAAGAAAACTGGAACACTAAACATAGCAGTGGTG +TTACCCGTGAACTCATGCGTGAGCTTAACGGAGGGGCATACACTCGCTATGTCGATAACAACTTCTGTGG +CCCTGATGGCTACCCTCTTGAGTGCATTAAAGACCTTCTAGCACGTGCTGGTAAAGCTTCATGCACTTTG +TCCGAACAACTGGACTTTATTGACACTAAGAGGGGTGTATACTGCTGCCGTGAACATGAGCATGAAATTG +CTTGGTACACGGAACGTTCTGAAAAGAGCTATGAATTGCAGACACCTTTTGAAATTAAATTGGCAAAGAA +ATTTGACACCTTCAATGGGGAATGTCCAAATTTTGTATTTCCCTTAAATTCCATAATCAAGACTATTCAA +CCAAGGGTTGAAAAGAAAAAGCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCCAGTTGCGTCAC +CAAATGAATGCAACCAAATGTGCCTTTCAACTCTCATGAAGTGTGATCATTGTGGTGAAACTTCATGGCA +GACGGGCGATTTTGTTAAAGCCACTTGCGAATTTTGTGGCACTGAGAATTTGACTAAAGAAGGTGCCACT +ACTTGTGGTTACTTACCCCAAAATGCTGTTGTTAAAATTTATTGTCCAGCATGTCACAATTCAGAAGTAG +GACCTGAGCATAGTCTTGCCGAATACCATAATGAATCTGGCTTGAAAACCATTCTTCGTAAGGGTGGTCG +CACTATTGCCTTTGGAGGCTGTGTGTTCTCTTATGTTGGTTGCCATAACAAGTGTGCCTATTGGGTTCCA +CGTGCTAGCGCTAACATAGGTTGTAACCATACAGGTGTTGTTGGAGAAGGTTCCGAAGGTCTTAATGACA +ACCTTCTTGAAATACTCCAAAAAGAGAAAGTCAACATCAATATTGTTGGTGACTTTAAACTTAATGAAGA +GATCGCCATTATTTTGGCATCTTTTTCTGCTTCCACAAGTGCTTTTGTGGAAACTGTGAAAGGTTTGGAT +TATAAAGCATTCAAACAAATTGTTGAATCCTGTGGTAATTTTAAAGTTACAAAAGGAAAAGCTAAAAAAG +GTGCCTGGAATATTGGTGAACAGAAATCAATACTGAGTCCTCTTTATGCATTTGCATCAGAGGCTGCTCG +TGTTGTACGATCAATTTTCTCCCGCACTCTTGAAACTGCTCAAAATTCTGTGCGTGTTTTACAGAAGGCC +GCTATAACAATACTAGATGGAATTTCACAGTATTCACTGAGACTCATTGATGCTATGATGTTCACATCTG +ATTTGGCTACTAACAATCTAGTTGTAATGGCCTACATTACAGGTGGTGTTGTTCAGTTGACTTCGCAGTG +GCTAACTAACATCTTTGGCACTGTTTATGAAAAACTCAAACCCGTCCTTGATTGGCTTGAAGAGAAGTTT +AAGGAAGGTGTAGAGTTTCTTAGAGACGGTTGGGAAATTGTTAAATTTATCTCAACCTGTGCTTGTGAAA +TTGTCGGTGGACAAATTGTCACCTGTGCAAAGGAAATTAAGGAGAGTGTTCAGACATTCTTTAAGCTTGT +AAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGCCTTGAATTTA +GGTGAAACATTTGTCACGCACTCAAAGGGATTGTACAGAAAGTGTGTTAAATCCAGAGAAGAAACTGGCC +TACTCATGCCTCTAAAAGCCCCAAAAGAAATTATCTTCTTAGAGGGAGAAACACTTCCCACAGAAGTGTT +AACAGAGGAAGTTGTCTTGAAAACTGGTGATTTACAACCATTAGAACAACCTACTAGTGAAGCTGTTGAA +GCTCCATTGGTTGGTACACCAGTTTGTATTAACGGGCTTATGTTGCTCGAAATCAAAGACACAGAAAAGT +ACTGTGCCCTTGCACCTAATATGATGGTAACAAACAATACCTTCACACTCAAAGGCGGTGCACCAACAAA +GGTTACTTTTGGTGATGACACTGTGATAGAAGTGCAAGGTTACAAGAGTGTGAATATCACTTTTGAACTT +GATGAAAGGATTGATAAAGTACTTAATGAGAAGTGCTCTGCCTATACAGTTGAACTCGGTACAGAAGTAA +ATGAGTTCGCCTGTGTTGTGGCAGATGCTGTCATAAAAACTTTGCAACCAGTATCTGAATTACTTACACC +ACTGGGCATTGATTTAGATGAGTGGAGTATGGCTACATACTACTTATTTGATGAGTCTGGTGAGTTTAAA +TTGGCTTCACATATGTATTGTTCTTTCTACCCTCCAGATGAGGATGAAGAAGAAGGTGATTGTGAAGAAG +AAGAGTTTGAGCCATCAACTCAATATGAGTATGGTACTGAAGATGATTACCAAGGTAAACCTTTGGAATT +TGGTGCCACTTCTGCTGCTCTTCAACCTGAAGAAGAGCAAGAAGAAGATTGGTTAGATGATGATAGTCAA +CAAACTGTTGGTCAACAAGACGGCAGTGAGGACAATCAGACAACTACTATTCAAACAATTGTTGAGGTTC +AACCTCAATTAGAGATGGAACTTACACCAGTTGTTCAGACTATTGAAGTGAATAGTTTTAGTGGTTATTT +AAAACTTACTGACAATGTATACATTAAAAATGCAGACATTGTGGAAGAAGCTAAAAAGGTAAAACCAACA +GTGGTTGTTAATGCAGCCAATGTTTACCTTAAACATGGAGGAGGTGTTGCAGGAGCCTTAAATAAGGCTA +CTAACAATGCCATGCAAGTTGAATCTGATGATTACATAGCTACTAATGGACCACTTAAAGTGGGTGGTAG +TTGTGTTTTAAGCGGACACAATCTTGCTAAACACTGTCTTCATGTTGTCGGCCCAAATGTTAACAAAGGT +GAAGACATTCAACTTCTTAAGAGTGCTTATGAAAATTTTAATCAGCACGAAGTTCTACTTGCACCATTAT +TATCAGCTGGTATTTTTGGTGCTGACCCTATACATTCTTTAAGAGTTTGTGTAGATACTGTTCGCACAAA +TGTCTACTTAGCTGTCTTTGATAAAAATCTCTATGACAAACTTGTTTCAAGCTTTTTGGAAATGAAGAGT +GAAAAGCAAGTTGAACAAAAGATCGCTGAGATTCCTAAAGAGGAAGTTAAGCCATTTATAACTGAAAGTA +AACCTTCAGTTGAACAGAGAAAACAAGATGATAAGAAAATCAAAGCTTGTGTTGAAGAAGTTACAACAAC +TCTGGAAGAAACTAAGTTCCTCACAGAAAACTTGTTACTTTATATTGACATTAATGGCAATCTTCATCCA +GATTCTGCCACTCTTGTTAGTGACATTGACATCACTTTCTTAAAGAAAGATGCTCCATATATAGTGGGTG +ATGTTGTTCAAGAGGGTGTTTTAACTGCTGTGGTTATACCTACTAAAAAGGCTGGTGGCACTACTGAAAT +GCTAGCGAAAGCTTTGAGAAAAGTGCCAACAGACAATTATATAACCACTTACCCGGGTCAGGGTTTAAAT +GGTTACACTGTAGAGGAGGCAAAGACAGTGCTTAAAAAGTGTAAAAGTGCCTTTTACATTCTACCATCTA +TTATCTCTAATGAGAAGCAAGAAATTCTTGGAACTGTTTCTTGGAATTTGCGAGAAATGCTTGCACATGC +AGAAGAAACACGCAAATTAATGCCTGTCTGTGTGGAAACTAAAGCCATAGTTTCAACTATACAGCGTAAA +TATAAGGGTATTAAAATACAAGAGGGTGTGGTTGATTATGGTGCTAGATTTTACTTTTACACCAGTAAAA +CAACTGTAGCGTCACTTATCAACACACTTAACGATCTAAATGAAACTCTTGTTACAATGCCACTTGGCTA +TGTAACACATGGCTTAAATTTGGAAGAAGCTGCTCGGTATATGAGATCTCTCAAAGTGCCAGCTACAGTT +TCTGTTTCTTCACCTGATGCTGTTACAGCGTATAATGGTTATCTTACTTCTTCTTCTAAAACACCTGAAG +AACATTTTATTGAAACCATCTCACTTGCTGGTTCCTATAAAGATTGGTCCTATTCTGGACAATCTACACA +ACTAGGTATAGAATTTCTTAAGAGAGGTGATAAAAGTGTATATTACACTAGTAATCCTACCACATTCCAC +CTAGATGGTGAAGTTATCACCTTTGACAATCTTAAGACACTTCTTTCTTTGAGAGAAGTGAGGACTATTA +AGGTGTTTACAACAGTAGACAACATTAACCTCCACACGCAAGTTGTGGACATGTCAATGACATATGGACA +ACAGTTTGGTCCAACTTATTTGGATGGAGCTGATGTTACTAAAATAAAACCTCATAATTCACATGAAGGT +AAAACATTTTATGTTTTACCTAATGATGACACTCTACGTGTTGAGGCTTTTGAGTACTACCACACAACTG +ATCCTAGTTTTCTGGGTAGGTACATGTCAGCATTAAATCACACTAAAAAGTGGAAATACCCACAAGTTAA +TGGTTTAACTTCTATTAAATGGGCAGATAACAACTGTTATCTTGCCACTGCATTGTTAACACTCCAACAA +ATAGAGTTGAAGTTTAATCCACCTGCTCTACAAGATGCTTATTACAGAGCAAGGGCTGGTGAAGCTGCTA +ACTTTTGTGCACTTATCTTAGCCTACTGTAATAAGACAGTAGGTGAGTTAGGTGATGTTAGAGAAACAAT +GAGTTACTTGTTTCAACATGCCAATTTAGATTCTTGCAAAAGAGTCTTGAACGTGGTGTGTAAAACTTGT +GGACAACAGCAGACAACCCTTAAGGGTGTAGAAGCTGTTATGTACATGGGCACACTTTCTTATGAACAAT +TTAAGAAAGGTGTTCAGATACCTTGTACGTGTGGTAAACAAGCTACAAAATATCTAGTACAACAGGAGTC +ACCTTTTGTTATGATGTCAGCACCACCTGCTCAGTATGAACTTAAGCATGGTACATTTACTTGTGCTAGT +GAGTACACTGGTAATTACCAGTGTGGTCACTATAAACATATAACTTCTAAAGAAACTTTGTATTGCATAG +ACGGTGCTTTACTTACAAAGTCCTCAGAATACAAAGGTCCTATTACGGATGTTTTCTACAAAGAAAACAG +TTACACAACAACCATAAAACCAGTTACTTATAAATTGGATGGTGTTGTTTGTACAGAAATTGACCCTAAG +TTGGACAATTATTATAAGAAAGACAATTCTTATTTCACAGAGCAACCAATTGATCTTGTACCAAACCAAC +CATATCCAAACGCAAGCTTCGATAATTTTAAGTTTGTATGTGATAATATCAAATTTGCTGATGATTTAAA +CCAGTTAACTGGTTATAAGAAACCTGCTTCAAGAGAGCTTAAAGTTACATTTTTCCCTGACTTAAATGGT +GATGTGGTGGCTATTGATTATAAACACTACACACCCTCTTTTAAGAAAGGAGCTAAATTGTTACATAAAC +CTATTGTTTGGCATGTTAACAATGCAACTAATAAAGCCACGTATAAACCAAATACCTGGTGTATACGTTG +TCTTTGGAGCACAAAACCAGTTGAAACATCAAATTCGTTTGATGTACTGAAGTCAGAGGACGCGCAGGGA +ATGGATAATCTTGCCTGCGAAGATCTAAAACCAGTCTCTGAAGAAGTAGTGGAAAATCCTACCATACAGA +AAGACGTTCTTGAGTGTAATGTGAAAACTACCGAAGTTGTAGGAGACATTATACTTAAACCAGCAAATAA +TAGTTTAAAAATTACAGAAGAGGTTGGCCACACAGATCTAATGGCTGCTTATGTAGACAATTCTAGTCTT +ACTATTAAGAAACCTAATGAATTATCTAGAGTATTAGGTTTGAAAACCCTTGCTACTCATGGTTTAGCTG +CTGTTAATAGTGTCCCTTGGGATACTATAGCTAATTATGCTAAGCCTTTTCTTAACAAAGTTGTTAGTAC +AACTACTAACATAGTTACACGGTGTTTAAACCGTGTTTGTACTAATTATATGCCTTATTTCTTTACTTTA +TTGCTACAATTGTGTACTTTTACTAGAAGTACAAATTCTAGAATTAAAGCATCTATGCCGACTACTATAG +CAAAGAATACTGTTAAGAGTGTCGGTAAATTTTGTCTAGAGGCTTCATTTAATTATTTGAAGTCACCTAA +TTTTTCTAAACTGATAAATATTATAATTTGGTTTTTACTATTAAGTGTTTGCCTAGGTTCTTTAATCTAC +TCAACCGCTGCTTTAGGTGTTTTAATGTCTAATTTAGGCATGCCTTCTTACTGTACTGGTTACAGAGAAG +GCTATTTGAACTCTACTAATGTCACTATTGCAACCTACTGTACTGGTTCTATACCTTGTAGTGTTTGTCT +TAGTGGTTTAGATTCTTTAGACACCTATCCTTCTTTAGAAACTATACAAATTACCATTTCATCTTTTAAA +TGGGATTTAACTGCTTTTGGCTTAGTTGCAGAGTGGTTTTTGGCATATATTCTTTTCACTAGGTTTTTCT +ATGTACTTGGATTGGCTGCAATCATGCAATTGTTTTTCAGCTATTTTGCAGTACATTTTATTAGTAATTC +TTGGCTTATGTGGTTAATAATTAATCTTGTACAAATGGCCCCGATTTCAGCTATGGTTAGAATGTACATC +TTCTTTGCATCATTTTATTATGTATGGAAAAGTTATGTGCATGTTGTAGACGGTTGTAATTCATCAACTT +GTATGATGTGTTACAAACGTAATAGAGCAACAAGAGTCGAATGTACAACTATTGTTAATGGTGTTAGAAG +GTCCTTTTATGTCTATGCTAATGGAGGTAAAGGCTTTTGCAAACTACACAATTGGAATTGTGTTAATTGT +GATACATTCTGTGCTGGTAGTACATTTATTAGTGATGAAGTTGCGAGAGACTTGTCACTACAGTTTAAAA +GACCAATAAATCCTACTGACCAGTCTTCTTACATCGTTGATAGTGTTACAGTGAAGAATGGTTCCATCCA +TCTTTACTTTGATAAAGCTGGTCAAAAGACTTATGAAAGACATTCTCTCTCTCATTTTGTTAACTTAGAC +AACCTGAGAGCTAATAACACTAAAGGTTCATTGCCTATTAATGTTATAGTTTTTGATGGTAAATCAAAAT +GTGAAGAATCATCTGCAAAATCAGCGTCTGTTTACTACAGTCAGCTTATGTGTCAACCTATACTGTTACT +AGATCAGGCATTAGTGTCTGATGTTGGTGATAGTGCGGAAGTTGCAGTTAAAATGTTTGATGCTTACGTT +AATACGTTTTCATCAACTTTTAACGTACCAATGGAAAAACTCAAAACACTAGTTGCAACTGCAGAAGCTG +AACTTGCAAAGAATGTGTCCTTAGACAATGTCTTATCTACTTTTATTTCAGCAGCTCGGCAAGGGTTTGT +TGATTCAGATGTAGAAACTAAAGATGTTGTTGAATGTCTTAAATTGTCACATCAATCTGACATAGAAGTT +ACTGGCGATAGTTGTAATAACTATATGCTCACCTATAACAAAGTTGAAAACATGACACCCCGTGACCTTG +GTGCTTGTATTGACTGTAGTGCGCGTCATATTAATGCGCAGGTAGCAAAAAGTCACAACATTGCTTTGAT +ATGGAACGTTAAAGATTTCATGTCATTGTCTGAACAACTACGAAAACAAATACGTAGTGCTGCTAAAAAG +AATAACTTACCTTTTAAGTTGACATGTGCAACTACTAGACAAGTTGTTAATGTTGTAACAACAAAGATAG +CACTTAAGGGTGGTAAAATTGTTAATAATTGGTTGAAGCAGTTAATTAAAGTTACACTTGTGTTCCTTTT +TGTTGCTGCTATTTTCTATTTAATAACACCTGTTCATGTCATGTCTAAACATACTGACTTTTCAAGTGAA +ATCATAGGATACAAGGCTATTGATGGTGGTGTCACTCGTGACATAGCATCTACAGATACTTGTTTTGCTA +ACAAACATGCTGATTTTGACACATGGTTTAGCCAGCGTGGTGGTAGTTATACTAATGACAAAGCTTGCCC +ATTGATTGCTGCAGTCATAACAAGAGAAGTGGGTTTTGTCGTGCCTGGTTTGCCTGGCACGATATTACGC +ACAACTAATGGTGACTTTTTGCATTTCTTACCTAGAGTTTTTAGTGCAGTTGGTAACATCTGTTACACAC +CATCAAAACTTATAGAGTACACTGACTTTGCAACATCAGCTTGTGTTTTGGCTGCTGAATGTACAATTTT +TAAAGATGCTTCTGGTAAGCCAGTACCATATTGTTATGATACCAATGTACTAGAAGGTTCTGTTGCTTAT +GAAAGTTTACGCCCTGACACACGTTATGTGCTCATGGATGGCTCTATTATTCAATTTCCTAACACCTACC +TTGAAGGTTCTGTTAGAGTGGTAACAACTTTTGATTCTGAGTACTGTAGGCACGGCACTTGTGAAAGATC +AGAAGCTGGTGTTTGTGTATCTACTAGTGGTAGATGGGTACTTAACAATGATTATTACAGATCTTTACCA +GGAGTTTTCTGTGGTGTAGATGCTGTAAATTTACTTACTAATATGTTTACACCACTAATTCAACCTATTG +GTGCTTTGGACATATCAGCATCTATAGTAGCTGGTGGTATTGTAGCTATCGTAGTAACATGCCTTGCCTA +CTATTTTATGAGGTTTAGAAGAGCTTTTGGTGAATACAGTCATGTAGTTGCCTTTAATACTTTACTATTC +CTTATGTCATTCACTGTACTCTGTTTAACACCAGTTTACTCATTCTTACCTGGTGTTTATTCTGTTATTT +ACTTGTACTTGACATTTTATCTTACTAATGATGTTTCTTTTTTAGCACATATTCAGTGGATGGTTATGTT +CACACCTTTAGTACCTTTCTGGATAACAATTGCTTATATCATTTGTATTTCCACAAAGCATTTCTATTGG +TTCTTTAGTAATTACCTAAAGAGACGTGTAGTCTTTAATGGTGTTTCCTTTAGTACTTTTGAAGAAGCTG +CGCTGTGCACCTTTTTGTTAAATAAAGAAATGTATCTAAAGTTGCGTAGTGATGTGCTATTACCTCTTAC +GCAATATAATAGATACTTAGCTCTTTATAATAAGTACAAGTATTTTAGTGGAGCAATGGATACAACTAGC +TACAGAGAAGCTGCTTGTTGTCATCTCGCAAAGGCTCTCAATGACTTCAGTAACTCAGGTTCTGATGTTC +TTTACCAACCACCACAAACCTCTATCACCTCAGCTGTTTTGCAGAGTGGTTTTAGAAAAATGGCATTCCC +ATCTGGTAAAGTTGAGGGTTGTATGGTACAAGTAACTTGTGGTACAACTACACTTAACGGTCTTTGGCTT +GATGACGTAGTTTACTGTCCAAGACATGTGATCTGCACCTCTGAAGACATGCTTAACCCTAATTATGAAG +ATTTACTCATTCGTAAGTCTAATCATAATTTCTTGGTACAGGCTGGTAATGTTCAACTCAGGGTTATTGG +ACATTCTATGCAAAATTGTGTACTTAAGCTTAAGGTTGATACAGCCAATCCTAAGACACCTAAGTATAAG +TTTGTTCGCATTCAACCAGGACAGACTTTTTCAGTGTTAGCTTGTTACAATGGTTCACCATCTGGTGTTT +ACCAATGTGCTATGAGGCCCAATTTCACTATTAAGGGTTCATTCCTTAATGGTTCATGTGGTAGTGTTGG +TTTTAACATAGATTATGACTGTGTCTCTTTTTGTTACATGCACCATATGGAATTACCAACTGGAGTTCAT +GCTGGCACAGACTTAGAAGGTAACTTTTATGGACCTTTTGTTGACAGGCAAACAGCACAAGCAGCTGGTA +CGGACACAACTATTACAGTTAATGTTTTAGCTTGGTTGTACGCTGCTGTTATAAATGGAGACAGGTGGTT +TCTCAATCGATTTACCACAACTCTTAATGACTTTAACCTTGTGGCTATGAAGTACAATTATGAACCTCTA +ACACAAGACCATGTTGACATACTAGGACCTCTTTCTGCTCAAACTGGAATTGCCGTTTTAGATATGTGTG +CTTCATTAAAAGAATTACTGCAAAATGGTATGAATGGACGTACCATATTGGGTAGTGCTTTATTAGAAGA +TGAATTTACACCTTTTGATGTTGTTAGACAATGCTCAGGTGTTACTTTCCAAAGTGCAGTGAAAAGAACA +ATCAAGGGTACACACCACTGGTTGTTACTCACAATTTTGACTTCACTTTTAGTTTTAGTCCAGAGTACTC +AATGGTCTTTGTTCTTTTTTTTGTATGAAAATGCCTTTTTACCTTTTGCTATGGGTATTATTGCTATGTC +TGCTTTTGCAATGATGTTTGTCAAACATAAGCATGCATTTCTCTGTTTGTTTTTGTTACCTTCTCTTGCC +ACTGTAGCTTATTTTAATATGGTCTATATGCCTGCTAGTTGGGTGATGCGTATTATGACATGGTTGGATA +TGGTTGATACTAGTTTGTCTGGTTTTAAGCTAAAAGACTGTGTTATGTATGCATCAGCTGTAGTGTTACT +AATCCTTATGACAGCAAGAACTGTGTATGATGATGGTGCTAGGAGAGTGTGGACACTTATGAATGTCTTG +ACACTCGTTTATAAAGTTTATTATGGTAATGCTTTAGATCAAGCCATTTCCATGTGGGCTCTTATAATCT +CTGTTACTTCTAACTACTCAGGTGTAGTTACAACTGTCATGTTTTTGGCCAGAGGTATTGTTTTTATGTG +TGTTGAGTATTGCCCTATTTTCTTCATAACTGGTAATACACTTCAGTGTATAATGCTAGTTTATTGTTTC +TTAGGCTATTTTTGTACTTGTTACTTTGGCCTCTTTTGTTTACTCAACCGCTACTTTAGACTGACTCTTG +GTGTTTATGATTACTTAGTTTCTACACAGGAGTTTAGATATATGAATTCACAGGGACTACTCCCACCCAA +GAATAGCATAGATGCCTTCAAACTCAACATTAAATTGTTGGGTGTTGGTGGCAAACCTTGTATCAAAGTA +GCCACTGTACAGTCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAAC +TCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAA +AGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTA +GACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAAGCTATAGCCTCAGAGTTTA +GTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGA +TTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCA +GCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTG +AGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAA +TGATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACA +ACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACAT +TTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAG +TGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCT +GCTGTCAAATTACAGAATAATGAGCTTAGTCCTGTTGCACTACGACAGATGTCTTGTGCTGCCGGTACTA +CACAAACTGCTTGCACTGATGACAATGCGTTAGCTTACTACAACACAACAAAGGGAGGTAGGTTTGTACT +TGCACTGTTATCCGATTTACAGGATTTGAAATGGGCTAGATTCCCTAAGAGTGATGGAACTGGTACTATC +TATACAGAACTGGAACCACCTTGTAGGTTTGTTACAGACACACCTAAAGGTCCTAAAGTGAAGTATTTAT +ACTTTATTAAAGGATTAAACAACCTAAATAGAGGTATGGTACTTGGTAGTTTAGCTGCCACAGTACGTCT +ACAAGCTGGTAATGCAACAGAAGTGCCTGCCAATTCAACTGTATTATCTTTCTGTGCTTTTGCTGTAGAT +GCTGCTAAAGCTTACAAAGATTATCTAGCTAGTGGGGGACAACCAATCACTAATTGTGTTAAGATGTTGT +GTACACACACTGGTACTGGTCAGGCAATAACAGTTACACCGGAAGCCAATATGGATCAAGAATCCTTTGG +TGGTGCATCGTGTTGTCTGTACTGCCGTTGCCACATAGATCATCCAAATCCTAAAGGATTTTGTGACTTA +AAAGGTAAGTATGTACAAATACCTACAACTTGTGCTAATGACCCTGTGGGTTTTACACTTAAAAACACAG +TCTGTACCGTCTGCGGTATGTGGAAAGGTTATGGCTGTAGTTGTGATCAACTCCGCGAACCCATGCTTCA +GTCAGCTGATGCACAATCGTTTTTAAACGGGTTTGCGGTGTAAGTGCAGCCCGTCTTACACCGTGCGGCA +CAGGCACTAGTACTGATGTCGTATACAGGGCTTTTGACATCTACAATGATAAAGTAGCTGGTTTTGCTAA +ATTCCTAAAAACTAATTGTTGTCGCTTCCAAGAAAAGGACGAAGATGACAATTTAATTGATTCTTACTTT +GTAGTTAAGAGACACACTTTCTCTAACTACCAACATGAAGAAACAATTTATAATTTACTTAAGGATTGTC +CAGCTGTTGCTAAACATGACTTCTTTAAGTTTAGAATAGACGGTGACATGGTACCACATATATCACGTCA +ACGTCTTACTAAATACACAATGGCAGACCTCGTCTATGCTTTAAGGCATTTTGATGAAGGTAATTGTGAC +ACATTAAAAGAAATACTTGTCACATACAATTGTTGTGATGATGATTATTTCAATAAAAAGGACTGGTATG +ATTTTGTAGAAAACCCAGATATATTACGCGTATACGCCAACTTAGGTGAACGTGTACGCCAAGCTTTGTT +AAAAACAGTACAATTCTGTGATGCCATGCGAAATGCTGGTATTGTTGGTGTACTGACATTAGATAATCAA +GATCTCAATGGTAACTGGTATGATTTCGGTGATTTCATACAAACCACGCCAGGTAGTGGAGTTCCTGTTG +TAGATTCTTATTATTCATTGTTAATGCCTATATTAACCTTGACCAGGGCTTTAACTGCAGAGTCACATGT +TGACACTGACTTAACAAAGCCTTACATTAAGTGGGATTTGTTAAAATATGACTTCACGGAAGAGAGGTTA +AAACTCTTTGACCGTTATTTTAAATATTGGGATCAGACATACCACCCAAATTGTGTTAACTGTTTGGATG +ACAGATGCATTCTGCATTGTGCAAACTTTAATGTTTTATTCTCTACAGTGTTCCCACCTACAAGTTTTGG +ACCACTAGTGAGAAAAATATTTGTTGATGGTGTTCCATTTGTAGTTTCAACTGGATACCACTTCAGAGAG +CTAGGTGTTGTACATAATCAGGATGTAAACTTACATAGCTCTAGACTTAGTTTTAAGGAATTACTTGTGT +ATGCTGCTGACCCTGCTATGCACGCTGCTTCTGGTAATCTATTACTAGATAAACGCACTACGTGCTTTTC +AGTAGCTGCACTTACTAACAATGTTGCTTTTCAAACTGTCAAACCCGGTAATTTTAACAAAGACTTCTAT +GACTTTGCTGTGTCTAAGGGTTTCTTTAAGGAAGGAAGTTCTGTTGAATTAAAACACTTCTTCTTTGCTC +AGGATGGTAATGCTGCTATCAGCGATTATGACTACTATCGTTATAATCTACCAACAATGTGTGATATCAG +ACAACTACTATTTGTAGTTGAAGTTGTTGATAAGTACTTTGATTGTTACGATGGTGGCTGTATTAATGCT +AACCAAGTCATCGTCAACAACCTAGACAAATCAGCTGGTTTTCCATTTAATAAATGGGGTAAGGCTAGAC +TTTATTATGATTCAATGAGTTATGAGGATCAAGATGCACTTTTCGCATATACAAAACGTAATGTCATCCC +TACTATAACTCAAATGAATCTTAAGTATGCCATTAGTGCAAAGAATAGAGCTCGCACCGTAGCTGGTGTC +TCTATCTGTAGTACTATGACCAATAGACAGTTTCATCAAAAATTATTGAAATCAATAGCCGCCACTAGAG +GAGCTACTGTAGTAATTGGAACAAGCAAATTCTATGGTGGTTGGCACAACATGTTAAAAACTGTTTATAG +TGATGTAGAAAACCCTCACCTTATGGGTTGGGATTATCCTAAATGTGATAGAGCCATGCCTAACATGCTT +AGAATTATGGCCTCACTTGTTCTTGCTCGCAAACATACAACGTGTTGTAGCTTGTCACACCGTTTCTATA +GATTAGCTAATGAGTGTGCTCAAGTATTGAGTGAAATGGTCATGTGTGGCGGTTCACTATATGTTAAACC +AGGTGGAACCTCATCAGGAGATGCCACAACTGCTTATGCTAATAGTGTTTTTAACATTTGTCAAGCTGTC +ACGGCCAATGTTAATGCACTTTTATCTACTGATGGTAACAAAATTGCCGATAAGTATGTCCGCAATTTAC +AACACAGACTTTATGAGTGTCTCTATAGAAATAGAGATGTTGACACAGACTTTGTGAATGAGTTTTACGC +ATATTTGCGTAAACATTTCTCAATGATGATACTCTCTGACGATGCTGTTGTGTGTTTCAATAGCACTTAT +GCATCTCAAGGTCTAGTGGCTAGCATAAAGAACTTTAAGTCAGTTCTTTATTATCAAAACAATGTTTTTA +TGTCTGAAGCAAAATGTTGGACTGAGACTGACCTTACTAAAGGACCTCATGAATTTTGCTCTCAACATAC +AATGCTAGTTAAACAGGGTGATGATTATGTGTACCTTCCTTACCCAGATCCATCAAGAATCCTAGGGGCC +GGCTGTTTTGTAGATGATATCGTAAAAACAGATGGTACACTTATGATTGAACGGTTCGTGTCTTTAGCTA +TAGATGCTTACCCACTTACTAAACATCCTAATCAGGAGTATGCTGATGTCTTTCATTTGTACTTACAATA +CATAAGAAAGCTACATGATGAGTTAACAGGACACATGTTAGACATGTATTCTGTTATGCTTACTAATGAT +AACACTTCAAGGTATTGGGAACCTGAGTTTTATGAGGCTATGTACACACCGCATACAGTCTTACAGGCTG +TTGGGGCTTGTGTTCTTTGCAATTCACAGACTTCATTAAGATGTGGTGCTTGCATACGTAGACCATTCTT +ATGTTGTAAATGCTGTTACGACCATGTCATATCAACATCACATAAATTAGTCTTGTCTGTTAATCCGTAT +GTTTGCAATGCTCCAGGTTGTGATGTCACAGATGTGACTCAACTTTACTTAGGAGGTATGAGCTATTATT +GTAAATCACATAAACCACCCATTAGTTTTCCATTGTGTGCTAATGGACAAGTTTTTGGTTTATATAAAAA +TACATGTGTTGGTAGCGATAATGTTACTGACTTTAATGCAATTGCAACATGTGACTGGACAAATGCTGGT +GATTACATTTTAGCTAACACCTGTACTGAAAGACTCAAGCTTTTTGCAGCAGAAACGCTCAAAGCTACTG +AGGAGACATTTAAACTGTCTTATGGTATTGCTACTGTACGTGAAGTGCTGTCTGACAGAGAATTACATCT +TTCATGGGAAGTTGGTAAACCTAGACCACCACTTAACCGAAATTATGTCTTTACTGGTTATCGTGTAACT +AAAAACAGTAAAGTACAAATAGGAGAGTACACCTTTGAAAAAGGTGACTATGGTGATGCTGTTGTTTACC +GAGGTACAACAACTTACAAATTAAATGTTGGTGATTATTTTGTGCTGACATCACATACAGTAATGCCATT +AAGTGCACCTACACTAGTGCCACAAGAGCACTATGTTAGAATTACTGGCTTATACCCAACACTCAATATC +TCAGATGAGTTTTCTAGCAATGTTGCAAATTATCAAAAGGTTGGTATGCAAAAGTATTCTACACTCCAGG +GACCACCTGGTACTGGTAAGAGTCATTTTGCTATTGGCCTAGCTCTCTACTACCCTTCTGCTCGCATAGT +GTATACAGCTTGCTCTCATGCCGCTGTTGATGCACTATGTGAGAAGGCATTAAAATATTTGCCTATAGAT +AAATGTAGTAGAATTATACCTGCACGTGCTCGTGTAGAGTGTTTTGATAAATTCAAAGTGAATTCAACAT +TAGAACAGTATGTCTTTTGTACTGTAAATGCATTGCCTGAGACGACAGCAGATATAGTTGTCTTTGATGA +AATTTCAATGGCCACAAATTATGATTTGAGTGTTGTCAATGCCAGATTACGTGCTAAGCACTATGTGTAC +ATTGGCGACCCTGCTCAATTACCTGCACCACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATT +TCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCC +TGCTGAAATTGTTGACACTGTGAGTGCTTTGGTTTATGATAATAAGCTTAAAGCACATAAAGACAAATCA +GCTCAATGCTTTAAAATGTTTTATAAGGGTGTTATCACGCATGATGTTTCATCTGCAATTAACAGGCCAC +AAATAGGCGTGGTAAGAGAATTCCTTACACGTAACCCTGCTTGGAGAAAAGCTGTCTTTATTTCACCTTA +TAATTCACAGAATGCTGTAGCCTCAAAGATTTTGGGACTACCAACTCAAACTGTTGATTCATCACAGGGC +TCAGAATATGACTATGTCATATTCACTCAAACCACTGAAACAGCTCACTCTTGTAATGTAAACAGATTTA +ATGTTGCTATTACCAGAGCAAAAGTAGGCATACTTTGCATAATGTCTGATAGAGACCTTTATGACAAGTT +GCAATTTACAAGTCTTGAAATTCCACGTAGGAATGTGGCAACTTTACAAGCTGAAAATGTAACAGGACTC +TTTAAAGATTGTAGTAAGGTAATCACTGGGTTACATCCTACACAGGCACCTACACACCTCAGTGTTGACA +CTAAATTCAAAACTGAAGGTTTATGTGTTGACATACCTGGCATACCTAAGGACATGACCTATAGAAGACT +CATCTCTATGATGGGTTTTAAAATGAATTATCAAGTTAATGGTTACCCTAACATGTTTATCACCCGCGAA +GAAGCTATAAGACATGTACGTGCATGGATTGGCTTCGATGTCGAGGGGTGTCATGCTACTAGAGAAGCTG +TTGGTACCAATTTACCTTTACAGCTAGGTTTTTCTACAGGTGTTAACCTAGTTGCTGTACCTACAGGTTA +TGTTGATACACCTAATAATACAGATTTTTCCAGAGTTAGTGCTAAACCACCGCCTGGAGATCAATTTAAA +CACCTCATACCACTTATGTACAAAGGACTTCCTTGGAATGTAGTGCGTATAAAGATTGTACAAATGTTAA +GTGACACACTTAAAAATCTCTCTGACAGAGTCGTATTTGTCTTATGGGCACATGGCTTTGAGTTGACATC +TATGAAGTATTTTGTGAAAATAGGACCTGAGCGCACCTGTTGTCTATGTGATAGACGTGCCACATGCTTT +TCCACTGCTTCAGACACTTATGCCTGTTGGCATCATTCTATTGGATTTGATTACGTCTATAATCCGTTTA +TGATTGATGTTCAACAATGGGGTTTTACAGGTAACCTACAAAGCAACCATGATCTGTATTGTCAAGTCCA +TGGTAATGCACATGTAGCTAGTTGTGATGCAATCATGACTAGGTGTCTAGCTGTCCACGAGTGCTTTGTT +AAGCGTGTTGACTGGACTATTGAATATCCTATAATTGGTGATGAACTGAAGATTAATGCGGCTTGTAGAA +AGGTTCAACACATGGTTGTTAAAGCTGCATTATTAGCAGACAAATTCCCAGTTCTTCACGACATTGGTAA +CCCTAAAGCTATTAAGTGTGTACCTCAAGCTGATGTAGAATGGAAGTTCTATGATGCACAGCCTTGTAGT +GACAAAGCTTATAAAATAGAAGAATTATTCTATTCTTATGCCACACATTCTGACAAATTCACAGATGGTG +TATGCCTATTTTGGAATTGCAATGTCGATAGATATCCTGCTAATTCCATTGTTTGTAGATTTGACACTAG +AGTGCTATCTAACCTTAACTTGCCTGGTTGTGATGGTGGCAGTTTGTATGTAAATAAACATGCATTCCAC +ACACCAGCTTTTGATAAAAGTGCTTTTGTTAATTTAAAACAATTACCATTTTTCTATTACTCTGACAGTC +CATGTGAGTCTCATGGAAAACAAGTAGTGTCAGATATAGATTATGTACCACTAAAGTCTGCTACGTGTAT +AACACGTTGCAATTTAGGTGGTGCTGTCTGTAGACATCATGCTAATGAGTACAGATTGTATCTCGATGCT +TATAACATGATGATCTCAGCTGGCTTTAGCTTGTGGGTTTACAAACAATTTGATACTTATAACCTCTGGA +ACACTTTTACAAGACTTCAGAGTTTAGAAAATGTGGCTTTTAATGTTGTAAATAAGGGACACTTTGATGG +ACAACAGGGTGAAGTACCAGTTTCTATCATTAATAACACTGTTTACACAAAAGTTGATGGTGTTGATGTA +GAATTGTTTGAAAATAAAACAACATTACCTGTTAATGTAGCATTTGAGCTTTGGGCTAAGCGCAACATTA +AACCAGTACCAGAGGTGAAAATACTCAATAATTTGGGTGTGGACATTGCTGCTAATACTGTGATCTGGGA +CTACAAAAGAGATGCTCCAGCACATATATCTACTATTGGTGTTTGTTCTATGACTGACATAGCCAAGAAA +CCAACTGAAACGATTTGTGCACCACTCACTGTCTTTTTTGATGGTAGAGTTGATGGTCAAGTAGACTTAT +TTAGAAATGCCCGTAATGGTGTTCTTATTACAGAAGGTAGTGTTAAAGGTTTACAACCATCTGTAGGTCC +CAAACAAGCTAGTCTTAATGGAGTCACATTAATTGGAGAAGCCGTAAAAACACAGTTCAATTATTATAAG +AAAGTTGATGGTGTTGTCCAACAATTACCTGAAACTTACTTTACTCAGAGTAGAAATTTACAAGAATTTA +AACCCAGGAGTCAAATGGAAATTGATTTCTTAGAATTAGCTATGGATGAATTCATTGAACGGTATAAATT +AGAAGGCTATGCCTTCGAACATATCGTTTATGGAGATTTTAGTCATAGTCAGTTAGGTGGTTTACATCTA +CTGATTGGACTAGCTAAACGTTTTAAGGAATCACCTTTTGAATTAGAAGATTTTATTCCTATGGACAGTA +CAGTTAAAAACTATTTCATAACAGATGCGCAAACAGGTTCATCTAAGTGTGTGTGTTCTGTTATTGATTT +ATTACTTGATGATTTTGTTGAAATAATAAAATCCCAAGATTTATCTGTAGTTTCTAAGGTTGTCAAAGTG +ACTATTGACTATACAGAAATTTCATTTATGCTTTGGTGTAAAGATGGCCATGTAGAAACATTTTACCCAA +AATTACAATCTAGTCAAGCGTGGCAACCGGGTGTTGCTATGCCTAATCTTTACAAAATGCAAAGAATGCT +ATTAGAAAAGTGTGACCTTCAAAATTATGGTGATAGTGCAACATTACCTAAAGGCATAATGATGAATGTC +GCAAAATATACTCAACTGTGTCAATATTTAAACACATTAACATTAGCTGTACCCTATAATATGAGAGTTA +TACATTTTGGTGCTGGTTCTGATAAAGGAGTTGCACCAGGTACAGCTGTTTTAAGACAGTGGTTGCCTAC +GGGTACGCTGCTTGTCGATTCAGATCTTAATGACTTTGTCTCTGATGCAGATTCAACTTTGATTGGTGAT +TGTGCAACTGTACATACAGCTAATAAATGGGATCTCATTATTAGTGATATGTACGACCCTAAGACTAAAA +ATGTTACAAAAGAAAATGACTCTAAAGAGGGTTTTTTCACTTACATTTGTGGGTTTATACAACAAAAGCT +AGCTCTTGGAGGTTCCGTGGCTATAAAGATAACAGAACATTCTTGGAATGCTGATCTTTATAAGCTCATG +GGACACTTCGCATGGTGGACAGCCTTTGTTACTAATGTGAATGCGTCATCATCTGAAGCATTTTTAATTG +GATGTAATTATCTTGGCAAACCACGCGAACAAATAGATGGTTATGTCATGCATGCAAATTACATATTTTG +GAGGAATACAAATCCAATTCAGTTGTCTTCCTATTCTTTATTTGACATGAGTAAATTTCCCCTTAAATTA +AGGGGTACTGCTGTTATGTCTTTAAAAGAAGGTCAAATCAATGATATGATTTTATCTCTTCTTAGTAAAG +GTAGACTTATAATTAGAGAAAACAACAGAGTTGTTATTTCTAGTGATGTTCTTGTTAACAACTAAACGAA +CAATGTTTGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACCAGAACTCA +ATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGACAAAGTTTTCAGATCCTCA +GTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCCAATGTTACTTGGTTCCATGCTATACATG +TCTCTGGGACCAATGGTACTAAGAGGTTTGATAACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGC +TTCCACTGAGAAGTCTAACATAATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCC +CTACTTATTGTTAATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATGATCCAT +TTTTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTATTCTAGTGC +GAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAAGGAAAACAGGGTAATTTC +AAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTATTTTAAAATATATTCTAAGCACACGCCTA +TTAATTTAGTGCGTGATCTCCCTCAGGGTTTTTCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTAT +TAACATCACTAGGTTTCAAACTTTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCA +GGTTGGACAGCTGGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATA +ATGAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAGTGTACGTT +GAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTCCAACCAACAGAATCTATT +GTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAAGTTTTTAACGCCACCAGATTTGCATCTG +TTTATGCTTGGAACAGGAAGAGAATCAGCAACTGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATC +ATTTTCCACTTTTAAGTGTTATGGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTAT +GCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTG +ATTATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAATCTTGATTC +TAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAATCTCAAACCTTTTGAGAGA +GATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGTAATGGTGTTGAAGGTTTTAATTGTTACT +TTCCTTTACAATCATATGGTTTCCAACCCACTAATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACT +TTCTTTTGAACTTCTACATGCACCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAAC +AAATGTGTCAATTTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTC +TGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAGACACTTGA +GATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCAGGAACAAATACTTCTAAC +CAGGTTGCTGTTCTTTATCAGGATGTTAACTGCACAGAAGTCCCTGTTGCTATTCATGCAGATCAACTTA +CTCCTACTTGGCGTGTTTATTCTACAGGTTCTAATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGC +TGAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACT +CAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTG +GTGCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATTAGTGTTAC +CACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATGTACATTTGTGGTGATTCA +ACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGTACACAATTAAACCGTGCTTTAACTGGAA +TAGCTGTTGAACAAGACAAAAACACCCAAGAAGTTTTTGCACAAGTCAAACAAATTTACAAAACACCACC +AATTAAAGATTTTGGTGGTTTTAATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCA +TTTATTGAAGATCTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATT +GCCTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTTTTGCCACC +TTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGTACAATCACTTCTGGTTGG +ACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATGCAAATGGCTTATAGGTTTAATGGTATTG +GAGTTACACAGAATGTTCTCTATGAGAACCAAAAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAA +AATTCAAGACTCACTTTCTTCCACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCA +CAAGCTTTAAACACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATA +TCCTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGACTTCAAAG +TTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCTTCTGCTAATCTTGCTGCT +ACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTTGATTTTTGTGGAAAGGGCTATCATCTTA +TGTCCTTCCCTCAGTCAGCACCTCATGGTGTAGTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAA +GAACTTCACAACTGCTCCTGCCATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTT +TCAAATGGCACACACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACA +CATTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCTTTGCAACC +TGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACATCACCAGATGTTGATTTA +GGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAAAAAGAAATTGACCGCCTCAATGAGGTTG +CCAAGAATTTAAATGAATCTCTCATCGATCTCCAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCC +ATGGTACATTTGGCTAGGTTTTATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGT +ATGACCAGTTGCTGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACG +ACTCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACATAAACGAACTTATGGATTTGTTTATGAGA +ATCTTCACAATTGGAACTGTAACTTTGAAGCAAGGTGAAATCAAGGATGCTACTCCTTCAGATTTTGTTC +GCGCTACTGCAACGATACCGATACAAGCCTCACTCCCTTTCGGATGGCTTATTGTTGGCGTTGCACTTCT +TGCTGTTTTTCAGAGCGCTTCCAAAATCATAACCCTCAAAAAGAGATGGCAACTAGCACTCTCCAAGGGT +GTTCACTTTGTTTGCAACTTGCTGTTGTTGTTTGTAACAGTTTACTCACACCTTTTGCTCGTTGCTGCTG +GCCTTGAAGCCCCTTTTCTCTATCTTTATGCTTTAGTCTACTTCTTGCAGAGTATAAACTTTGTAAGAAT +AATAATGAGGCTTTGGCTTTGCTGGAAATGCCGTTCCAAAAACCCATTACTTTATGATGCCAACTATTTT +CTTTGCTGGCATACTAATTGTTACGACTATTGTATACCTTACAATAGTGTAACTTCTTCAATTGTCATTA +CTTCAGGTGATGGCACAACAAGTCCTATTTCTGAACATGACTACCAGATTGGTGGTTATACTGAAAAATG +GGAATCTGGAGTAAAAGACTGTGTTGTATTACACAGTTACTTCACTTCAGACTATTACCAGCTGTACTCA +ACTCAATTGAGTACAGACACTGGTGTTGAACATGTTACCTTCTTCATCTACAATAAAATTGTTGATGAGC +CTGAAGAACATGTCCAAATTCACACAATCGACGGTTCATCCGGAGTTGTTAATCCAGTAATGGAACCAAT +TTATGATGAACCGACGACGACTACTAGCGTGCCTTTGTAAGCACAAGCTGATGAGTACGAACTTATGTAC +TCATTCGTTTCGGAAGAGACAGGTACGTTAATAGTTAATAGCGTACTTCTTTTTCTTGCTTTCGTGGTAT +TCTTGCTAGTTACACTAGCCATCCTTACTGCGCTTCGATTGTGTGCGTACTGCTGCAATATTGTTAACGT +GAGTCTTGTAAAACCTTCTTTTTACGTTTACTCTCGTGTTAAAAATCTGAATTCTTCTAGAGTTCCTGAT +CTTCTGGTCTAAACGAACTAAATATTATATTAGTTTTTCTGTTTGGAACTTTAATTTTAGCCATGGCAGA +TTCCAACGGTACTATTACCGTTGAAGAGCTTAAAAAGCTCCTTGAACAATGGAACCTAGTAATAGGTTTC +CTATTCCTTACATGGATTTGTCTTCTACAATTTGCCTATGCCAACAGGAATAGGTTTTTGTATATAATTA +AGTTAATTTTCCTCTGGCTGTTATGGCCAGTAACTTTAGCTTGTTTTGTGCTTGCTGCTGTTTACAGAAT +AAATTGGATCACCGGTGGAATTGCTATCGCAATGGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTC +ATTGCTTCTTTCAGACTGTTTGCGCGTACGCGTTCCATGTGGTCATTCAATCCAGAAACTAACATTCTTC +TCAACGTGCCACTCCATGGCACTATTCTGACCAGACCGCTTCTAGAAAGTGAACTCGTAATCGGAGCTGT +GATCCTTCGTGGACATCTTCGTATTGCTGGACACCATCTAGGACGCTGTGACATCAAGGACCTGCCTAAA +GAAATCACTGTTGCTACATCACGAACGCTTTCTTATTACAAATTGGGAGCTTCGCAGCGTGTAGCAGGTG +ACTCAGGTTTTGCTGCATACAGTCGCTACAGGATTGGCAACTATAAATTAAACACAGACCATTCCAGTAG +CAGTGACAATATTGCTTTGCTTGTACAGTAAGTGACAACAGATGTTTCATCTCGTTGACTTTCAGGTTAC +TATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATA +AACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAAC +CAATGGAGATTGATTAAACGAACATGAAAATTATTCTTTTCTTGGCACTGATAACACTCGCTACTTGTGA +GCTTTATCACTACCAAGAGTGTGTTAGAGGTACAACAGTACTTTTAAAAGAACCTTGCTCTTCTGGAACA +TACGAGGGCAATTCACCATTTCATCCTCTAGCTGATAACAAATTTGCACTGACTTGCTTTAGCACTCAAT +TTGCTTTTGCTTGTCCTGACGGCGTAAAACACGTCTATCAGTTACGTGCCAGATCAGTTTCACCTAAACT +GTTCATCAGACAAGAGGAAGTTCAAGAACTTTACTCTCCAATTTTTCTTATTGTTGCGGCAATAGTGTTT +ATAACACTTTGCTTCACACTCAAAAGAAAGACAGAATGATTGAACTTTCATTAATTGACTTCTATTTGTG +CTTTTTAGCCTTTCTGCTATTCCTTGTTTTAATTATGCTTATTATCTTTTGGTTCTCACTTGAACTGCAA +GATCATAATGAAACTTGTCACGCCTAAACGAACATGAAATTTCTTGTTTTCTTAGGAATCATCACAACTG +TAGCTGCATTTCACCAAGAATGTAGTTTACAGTCATGTACTCAACATCAACCATATGTAGTTGATGACCC +GTGTCCTATTCACTTCTATTCTAAATGGTATATTAGAGTAGGAGCTAGAAAATCAGCACCTTTAATTGAA +TTGTGCGTGGATGAGGCTGGTTCTAAATCACCCATTCAGTACATCGATATCGGTAATTATACAGTTTCCT +GTTTACCTTTTACAATTAATTGCCAGGAACCTAAATTGGGTAGTCTTGTAGTGCGTTGTTCGTTCTATGA +AGACTTTTTAGAGTATCATGACGTTCGTGTTGTTTTAGATTTCATCTAAACGAACAAACTAAAATGTCTG +ATAATGGACCCCAAAATCAGCGAAATGCACCCCGCATTACGTTTGGTGGACCCTCAGATTCAACTGGCAG +TAACCAGAATGGAGAACGCAGTGGGGCGCGATCAAAACAACGTCGGCCCCAAGGTTTACCCAATAATACT +GCGTCTTGGTTCACCGCTCTCACTCAACATGGCAAGGAAGACCTTAAATTCCCTCGAGGACAAGGCGTTC +CAATTAACACCAATAGCAGTCCAGATGACCAAATTGGCTACTACCGAAGAGCTACCAGACGAATTCGTGG +TGGTGACGGTAAAATGAAAGATCTCAGTCCAAGATGGTATTTCTACTACCTAGGAACTGGGCCAGAAGCT +GGACTTCCCTATGGTGCTAACAAAGACGGCATCATATGGGTTGCAACTGAGGGAGCCTTGAATACACCAA +AAGATCACATTGGCACCCGCAATCCTGCTAACAATGCTGCAATCGTGCTACAACTTCCTCAAGGAACAAC +ATTGCCAAAAGGCTTCTACGCAGAAGGGAGCAGAGGCGGCAGTCAAGCCTCTTCTCGTTCCTCATCACGT +AGTCGCAACAGTTCAAGAAATTCAACTCCAGGCAGCAGTAGGGGAACTTCTCCTGCTAGAATGGCTGGCA +ATGGCGGTGATGCTGCTCTTGCTTTGCTGCTGCTTGACAGATTGAACCAGCTTGAGAGCAAAATGTCTGG +TAAAGGCCAACAACAACAAGGCCAAACTGTCACTAAGAAATCTGCTGCTGAGGCTTCTAAGAAGCCTCGG +CAAAAACGTACTGCCACTAAAGCATACAATGTAACACAAGCTTTCGGCAGACGTGGTCCAGAACAAACCC +AAGGAAATTTTGGGGACCAGGAACTAATCAGACAAGGAACTGATTACAAACATTGGCCGCAAATTGCACA +ATTTGCCCCCAGCGCTTCAGCGTTCTTCGGAATGTCGCGCATTGGCATGGAAGTCACACCTTCGGGAACG +TGGTTGACCTACACAGGTGCCATCAAATTGGATGACAAAGATCCAAATTTCAAAGATCAAGTCATTTTGC +TGAATAAGCATATTGACGCATACAAAACATTCCCACCAACAGAGCCTAAAAAGGACAAAAAGAAGAAGGC +TGATGAAACTCAAGCCTTACCGCAGAGACAGAAGAAACAGCAAACTGTGACTCTTCTTCCTGCTGCAGAT +TTGGATGATTTCTCCAAACAATTGCAACAATCCATGAGCAGTGCTGACTCAACTCAGGCCTAAACTCATG +CAGACCACACAAGGCAGATGGGCTATATAAACGTTTTCGCTTTTCCGTTTACGATATATAGTCTACTCTT +GTGCAGAATGAATTCTCGTAACTACATAGCACAAGTAGATGTAGTTAACTTTAATCTCACATAGCAATCT +TTAATCAGTGTGTAACATTAGGGAGGACTTGAAAGAGCCACCACATTTTCACCGAGGCCACGCGGAGTAC +GATCGAGTGTACAGTGAACAATGCTAGGGAGAGCTGCCTATATGGAAGAGCCCTAATGTGTAAAATTAAT +TTTAGTAGTGCTATCCCCATGTGATTTTAATAGCTTCTTAGGAGAATGACAAAAAAAAAAAAAAAAAAAA +AAAAAAAAAAAAA diff --git a/test/data/broken/primer-bounds/info.yml b/test/data/broken/primer-bounds/info.yml new file mode 100644 index 0000000..133ad6c --- /dev/null +++ b/test/data/broken/primer-bounds/info.yml @@ -0,0 +1,20 @@ +schema_version: 1.0.0-alpha +name: eden +amplicon_size: 2500 +version: v1 +organism: sars-cov-2 +aliases: +- sydney +developers: +- John-Sebastian Eden +- Eby Sim +definition_url: https://github.com/pha4ge/primer-schemes/tree/main/sars-cov-2/eden/v1 +citations: +- https://www.protocols.io/view/sars-cov-2-genome-sequencing-using-long-pooled-amp-kxygxeob4v8j/v1 +notes: +- Protocol includes addendum for ONT sequencing +license: CC-BY-4.0 +citations: + - https://dx.doi.org/10.17504/protocols.io.befyjbpw +primer_checksum: primaschema:55c9726eb1400cab +reference_checksum: primaschema:b1acd7163146bf17 diff --git a/test/data/broken/primer-bounds/primer.bed b/test/data/broken/primer-bounds/primer.bed new file mode 100644 index 0000000..9793fd7 --- /dev/null +++ b/test/data/broken/primer-bounds/primer.bed @@ -0,0 +1,28 @@ +MN908947.3 31 55 SARS2_1_LEFT_1 1 + CCAACCAACTTTCGATCTCTTGTA +MN908947.3 2569 2593 SARS2_1_RIGHT_1 1 - AGCTTCAACAGCTTCACTAGTAGG +MN908947.3 1876 1898 SARS2_2_LEFT_1 2 + TCAGAGGCTGCTCGTGTTGTAC +MN908947.3 4429 4451 SARS2_2_RIGHT_1 2 - TAGTTTCCACACAGACAGGCAT +MN908947.3 4295 4322 SARS2_3_LEFT_1 1 + CAGTGCTTAAAAAGTGTAAAAGTGCCT +MN908947.3 6847 6874 SARS2_3_RIGHT_1 1 - AACAGTATTCTTTGCTATAGTAGTCGG +MN908947.3 6287 6311 SARS2_4_LEFT_1 2 + GGTGTATACGTTGTCTTTGGAGCA +MN908947.3 8828 8852 SARS2_4_RIGHT_1 2 - CCACTTCTCTTGTTATGACTGCAG +MN908947.3 8596 8620 SARS2_5_LEFT_1 1 + CTTGTGTTCCTTTTTGTTGCTGCT +MN908947.3 11049 11075 SARS2_5_RIGHT_1 1 - AGAACAAAGACCATTGAGTACTCTGG +MN908947.3 10363 10385 SARS2_6_LEFT_1 2 + GTTCGCATTCAACCAGGACAGA +MN908947.3 12780 12803 SARS2_6_RIGHT_1 2 - ACCTACCTCCCTTTGTTGTGTTG +MN908947.3 12711 12733 SARS2_7_LEFT_1 1 + ACGACAGATGTCTTGTGCTGCC +MN908947.3 15225 15247 SARS2_7_RIGHT_1 1 - TTAACATGTTGTGCCAACCACC +MN908947.3 14546 14571 SARS2_8_LEFT_1 2 + GGAATTACTTGTGTATGCTGCTGAC +MN908947.3 17131 17153 SARS2_8_RIGHT_1 2 - TACACTATGCGAGCAGAAGGGT +MN908947.3 16847 16872 SARS2_9_LEFT_1 1 + CTATGGTGATGCTGTTGTTTACCGA +MN908947.3 19254 19279 SARS2_9_RIGHT_1 1 - AACCAGGCAAGTTAAGGTTAGATAG +MN908947.3 18897 18919 SARS2_10_LEFT_1 2 + GTTAAGCGTGTTGACTGGACTA +MN908947.3 21428 21456 SARS2_10_RIGHT_1 2 - TTGACCTTCTTTTAAAGACATAACAGCA +MN908947.3 21358 21387 SARS2_11_LEFT_1 1 + CAAATCCAATTCAGTTGTCTTCCTATTCT +MN908947.3 23823 23848 SARS2_11_RIGHT_1 1 - TTGTGTACAAAAACTGCCATATTGC +MN908947.3 23123 23145 SARS2_12_LEFT_1 2 + CAGCAACTGTTTGTGGACCTAA +MN908947.3 25647 25674 SARS2_12_RIGHT_1 2 - AAGGTGTGAGTAAACTGTTACAAACAA +MN908947.3 25602 25624 SARS2_13_LEFT_1 1 + CTAGCACTCTCCAAGGGTGTTC +MN908947.3 28146 28173 SARS2_13_RIGHT_1 1 - TAGGTTCCTGGCAATTAATTGTAAAAG +MN908947.3 27447 27472 SARS2_14_LEFT_1 2 + CACTACCAAGAGTGTGTTAGAGGTA +MN908947.3 32000 32030 SARS2_14_RIGHT_1 2 - ATTCTCCTAAGAAGCTATTAAAATCACATG diff --git a/test/data/broken/primer-bounds/reference.fasta b/test/data/broken/primer-bounds/reference.fasta new file mode 100644 index 0000000..e1cfd92 --- /dev/null +++ b/test/data/broken/primer-bounds/reference.fasta @@ -0,0 +1,429 @@ +>MN908947.3 +ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAA +CGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAAC +TAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTG +TTGCAGCCGATCATCAGCACATCTAGGTTTCGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTC +CCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTAC +GTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGG +CTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAAACGTTCGGAT +GCTCGAACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACTCGAAGGCATTCAGTACGGTC +GTAGTGGTGAGACACTTGGTGTCCTTGTCCCTCATGTGGGCGAAATACCAGTGGCTTACCGCAAGGTTCT +TCTTCGTAAGAACGGTAATAAAGGAGCTGGTGGCCATAGTTACGGCGCCGATCTAAAGTCATTTGACTTA +GGCGACGAGCTTGGCACTGATCCTTATGAAGATTTTCAAGAAAACTGGAACACTAAACATAGCAGTGGTG +TTACCCGTGAACTCATGCGTGAGCTTAACGGAGGGGCATACACTCGCTATGTCGATAACAACTTCTGTGG +CCCTGATGGCTACCCTCTTGAGTGCATTAAAGACCTTCTAGCACGTGCTGGTAAAGCTTCATGCACTTTG +TCCGAACAACTGGACTTTATTGACACTAAGAGGGGTGTATACTGCTGCCGTGAACATGAGCATGAAATTG +CTTGGTACACGGAACGTTCTGAAAAGAGCTATGAATTGCAGACACCTTTTGAAATTAAATTGGCAAAGAA +ATTTGACACCTTCAATGGGGAATGTCCAAATTTTGTATTTCCCTTAAATTCCATAATCAAGACTATTCAA +CCAAGGGTTGAAAAGAAAAAGCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCCAGTTGCGTCAC +CAAATGAATGCAACCAAATGTGCCTTTCAACTCTCATGAAGTGTGATCATTGTGGTGAAACTTCATGGCA +GACGGGCGATTTTGTTAAAGCCACTTGCGAATTTTGTGGCACTGAGAATTTGACTAAAGAAGGTGCCACT +ACTTGTGGTTACTTACCCCAAAATGCTGTTGTTAAAATTTATTGTCCAGCATGTCACAATTCAGAAGTAG +GACCTGAGCATAGTCTTGCCGAATACCATAATGAATCTGGCTTGAAAACCATTCTTCGTAAGGGTGGTCG +CACTATTGCCTTTGGAGGCTGTGTGTTCTCTTATGTTGGTTGCCATAACAAGTGTGCCTATTGGGTTCCA +CGTGCTAGCGCTAACATAGGTTGTAACCATACAGGTGTTGTTGGAGAAGGTTCCGAAGGTCTTAATGACA +ACCTTCTTGAAATACTCCAAAAAGAGAAAGTCAACATCAATATTGTTGGTGACTTTAAACTTAATGAAGA +GATCGCCATTATTTTGGCATCTTTTTCTGCTTCCACAAGTGCTTTTGTGGAAACTGTGAAAGGTTTGGAT +TATAAAGCATTCAAACAAATTGTTGAATCCTGTGGTAATTTTAAAGTTACAAAAGGAAAAGCTAAAAAAG +GTGCCTGGAATATTGGTGAACAGAAATCAATACTGAGTCCTCTTTATGCATTTGCATCAGAGGCTGCTCG +TGTTGTACGATCAATTTTCTCCCGCACTCTTGAAACTGCTCAAAATTCTGTGCGTGTTTTACAGAAGGCC +GCTATAACAATACTAGATGGAATTTCACAGTATTCACTGAGACTCATTGATGCTATGATGTTCACATCTG +ATTTGGCTACTAACAATCTAGTTGTAATGGCCTACATTACAGGTGGTGTTGTTCAGTTGACTTCGCAGTG +GCTAACTAACATCTTTGGCACTGTTTATGAAAAACTCAAACCCGTCCTTGATTGGCTTGAAGAGAAGTTT +AAGGAAGGTGTAGAGTTTCTTAGAGACGGTTGGGAAATTGTTAAATTTATCTCAACCTGTGCTTGTGAAA +TTGTCGGTGGACAAATTGTCACCTGTGCAAAGGAAATTAAGGAGAGTGTTCAGACATTCTTTAAGCTTGT +AAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGCCTTGAATTTA +GGTGAAACATTTGTCACGCACTCAAAGGGATTGTACAGAAAGTGTGTTAAATCCAGAGAAGAAACTGGCC +TACTCATGCCTCTAAAAGCCCCAAAAGAAATTATCTTCTTAGAGGGAGAAACACTTCCCACAGAAGTGTT +AACAGAGGAAGTTGTCTTGAAAACTGGTGATTTACAACCATTAGAACAACCTACTAGTGAAGCTGTTGAA +GCTCCATTGGTTGGTACACCAGTTTGTATTAACGGGCTTATGTTGCTCGAAATCAAAGACACAGAAAAGT +ACTGTGCCCTTGCACCTAATATGATGGTAACAAACAATACCTTCACACTCAAAGGCGGTGCACCAACAAA +GGTTACTTTTGGTGATGACACTGTGATAGAAGTGCAAGGTTACAAGAGTGTGAATATCACTTTTGAACTT +GATGAAAGGATTGATAAAGTACTTAATGAGAAGTGCTCTGCCTATACAGTTGAACTCGGTACAGAAGTAA +ATGAGTTCGCCTGTGTTGTGGCAGATGCTGTCATAAAAACTTTGCAACCAGTATCTGAATTACTTACACC +ACTGGGCATTGATTTAGATGAGTGGAGTATGGCTACATACTACTTATTTGATGAGTCTGGTGAGTTTAAA +TTGGCTTCACATATGTATTGTTCTTTCTACCCTCCAGATGAGGATGAAGAAGAAGGTGATTGTGAAGAAG +AAGAGTTTGAGCCATCAACTCAATATGAGTATGGTACTGAAGATGATTACCAAGGTAAACCTTTGGAATT +TGGTGCCACTTCTGCTGCTCTTCAACCTGAAGAAGAGCAAGAAGAAGATTGGTTAGATGATGATAGTCAA +CAAACTGTTGGTCAACAAGACGGCAGTGAGGACAATCAGACAACTACTATTCAAACAATTGTTGAGGTTC +AACCTCAATTAGAGATGGAACTTACACCAGTTGTTCAGACTATTGAAGTGAATAGTTTTAGTGGTTATTT +AAAACTTACTGACAATGTATACATTAAAAATGCAGACATTGTGGAAGAAGCTAAAAAGGTAAAACCAACA +GTGGTTGTTAATGCAGCCAATGTTTACCTTAAACATGGAGGAGGTGTTGCAGGAGCCTTAAATAAGGCTA +CTAACAATGCCATGCAAGTTGAATCTGATGATTACATAGCTACTAATGGACCACTTAAAGTGGGTGGTAG +TTGTGTTTTAAGCGGACACAATCTTGCTAAACACTGTCTTCATGTTGTCGGCCCAAATGTTAACAAAGGT +GAAGACATTCAACTTCTTAAGAGTGCTTATGAAAATTTTAATCAGCACGAAGTTCTACTTGCACCATTAT +TATCAGCTGGTATTTTTGGTGCTGACCCTATACATTCTTTAAGAGTTTGTGTAGATACTGTTCGCACAAA +TGTCTACTTAGCTGTCTTTGATAAAAATCTCTATGACAAACTTGTTTCAAGCTTTTTGGAAATGAAGAGT +GAAAAGCAAGTTGAACAAAAGATCGCTGAGATTCCTAAAGAGGAAGTTAAGCCATTTATAACTGAAAGTA +AACCTTCAGTTGAACAGAGAAAACAAGATGATAAGAAAATCAAAGCTTGTGTTGAAGAAGTTACAACAAC +TCTGGAAGAAACTAAGTTCCTCACAGAAAACTTGTTACTTTATATTGACATTAATGGCAATCTTCATCCA +GATTCTGCCACTCTTGTTAGTGACATTGACATCACTTTCTTAAAGAAAGATGCTCCATATATAGTGGGTG +ATGTTGTTCAAGAGGGTGTTTTAACTGCTGTGGTTATACCTACTAAAAAGGCTGGTGGCACTACTGAAAT +GCTAGCGAAAGCTTTGAGAAAAGTGCCAACAGACAATTATATAACCACTTACCCGGGTCAGGGTTTAAAT +GGTTACACTGTAGAGGAGGCAAAGACAGTGCTTAAAAAGTGTAAAAGTGCCTTTTACATTCTACCATCTA +TTATCTCTAATGAGAAGCAAGAAATTCTTGGAACTGTTTCTTGGAATTTGCGAGAAATGCTTGCACATGC +AGAAGAAACACGCAAATTAATGCCTGTCTGTGTGGAAACTAAAGCCATAGTTTCAACTATACAGCGTAAA +TATAAGGGTATTAAAATACAAGAGGGTGTGGTTGATTATGGTGCTAGATTTTACTTTTACACCAGTAAAA +CAACTGTAGCGTCACTTATCAACACACTTAACGATCTAAATGAAACTCTTGTTACAATGCCACTTGGCTA +TGTAACACATGGCTTAAATTTGGAAGAAGCTGCTCGGTATATGAGATCTCTCAAAGTGCCAGCTACAGTT +TCTGTTTCTTCACCTGATGCTGTTACAGCGTATAATGGTTATCTTACTTCTTCTTCTAAAACACCTGAAG +AACATTTTATTGAAACCATCTCACTTGCTGGTTCCTATAAAGATTGGTCCTATTCTGGACAATCTACACA +ACTAGGTATAGAATTTCTTAAGAGAGGTGATAAAAGTGTATATTACACTAGTAATCCTACCACATTCCAC +CTAGATGGTGAAGTTATCACCTTTGACAATCTTAAGACACTTCTTTCTTTGAGAGAAGTGAGGACTATTA +AGGTGTTTACAACAGTAGACAACATTAACCTCCACACGCAAGTTGTGGACATGTCAATGACATATGGACA +ACAGTTTGGTCCAACTTATTTGGATGGAGCTGATGTTACTAAAATAAAACCTCATAATTCACATGAAGGT +AAAACATTTTATGTTTTACCTAATGATGACACTCTACGTGTTGAGGCTTTTGAGTACTACCACACAACTG +ATCCTAGTTTTCTGGGTAGGTACATGTCAGCATTAAATCACACTAAAAAGTGGAAATACCCACAAGTTAA +TGGTTTAACTTCTATTAAATGGGCAGATAACAACTGTTATCTTGCCACTGCATTGTTAACACTCCAACAA +ATAGAGTTGAAGTTTAATCCACCTGCTCTACAAGATGCTTATTACAGAGCAAGGGCTGGTGAAGCTGCTA +ACTTTTGTGCACTTATCTTAGCCTACTGTAATAAGACAGTAGGTGAGTTAGGTGATGTTAGAGAAACAAT +GAGTTACTTGTTTCAACATGCCAATTTAGATTCTTGCAAAAGAGTCTTGAACGTGGTGTGTAAAACTTGT +GGACAACAGCAGACAACCCTTAAGGGTGTAGAAGCTGTTATGTACATGGGCACACTTTCTTATGAACAAT +TTAAGAAAGGTGTTCAGATACCTTGTACGTGTGGTAAACAAGCTACAAAATATCTAGTACAACAGGAGTC +ACCTTTTGTTATGATGTCAGCACCACCTGCTCAGTATGAACTTAAGCATGGTACATTTACTTGTGCTAGT +GAGTACACTGGTAATTACCAGTGTGGTCACTATAAACATATAACTTCTAAAGAAACTTTGTATTGCATAG +ACGGTGCTTTACTTACAAAGTCCTCAGAATACAAAGGTCCTATTACGGATGTTTTCTACAAAGAAAACAG +TTACACAACAACCATAAAACCAGTTACTTATAAATTGGATGGTGTTGTTTGTACAGAAATTGACCCTAAG +TTGGACAATTATTATAAGAAAGACAATTCTTATTTCACAGAGCAACCAATTGATCTTGTACCAAACCAAC +CATATCCAAACGCAAGCTTCGATAATTTTAAGTTTGTATGTGATAATATCAAATTTGCTGATGATTTAAA +CCAGTTAACTGGTTATAAGAAACCTGCTTCAAGAGAGCTTAAAGTTACATTTTTCCCTGACTTAAATGGT +GATGTGGTGGCTATTGATTATAAACACTACACACCCTCTTTTAAGAAAGGAGCTAAATTGTTACATAAAC +CTATTGTTTGGCATGTTAACAATGCAACTAATAAAGCCACGTATAAACCAAATACCTGGTGTATACGTTG +TCTTTGGAGCACAAAACCAGTTGAAACATCAAATTCGTTTGATGTACTGAAGTCAGAGGACGCGCAGGGA +ATGGATAATCTTGCCTGCGAAGATCTAAAACCAGTCTCTGAAGAAGTAGTGGAAAATCCTACCATACAGA +AAGACGTTCTTGAGTGTAATGTGAAAACTACCGAAGTTGTAGGAGACATTATACTTAAACCAGCAAATAA +TAGTTTAAAAATTACAGAAGAGGTTGGCCACACAGATCTAATGGCTGCTTATGTAGACAATTCTAGTCTT +ACTATTAAGAAACCTAATGAATTATCTAGAGTATTAGGTTTGAAAACCCTTGCTACTCATGGTTTAGCTG +CTGTTAATAGTGTCCCTTGGGATACTATAGCTAATTATGCTAAGCCTTTTCTTAACAAAGTTGTTAGTAC +AACTACTAACATAGTTACACGGTGTTTAAACCGTGTTTGTACTAATTATATGCCTTATTTCTTTACTTTA +TTGCTACAATTGTGTACTTTTACTAGAAGTACAAATTCTAGAATTAAAGCATCTATGCCGACTACTATAG +CAAAGAATACTGTTAAGAGTGTCGGTAAATTTTGTCTAGAGGCTTCATTTAATTATTTGAAGTCACCTAA +TTTTTCTAAACTGATAAATATTATAATTTGGTTTTTACTATTAAGTGTTTGCCTAGGTTCTTTAATCTAC +TCAACCGCTGCTTTAGGTGTTTTAATGTCTAATTTAGGCATGCCTTCTTACTGTACTGGTTACAGAGAAG +GCTATTTGAACTCTACTAATGTCACTATTGCAACCTACTGTACTGGTTCTATACCTTGTAGTGTTTGTCT +TAGTGGTTTAGATTCTTTAGACACCTATCCTTCTTTAGAAACTATACAAATTACCATTTCATCTTTTAAA +TGGGATTTAACTGCTTTTGGCTTAGTTGCAGAGTGGTTTTTGGCATATATTCTTTTCACTAGGTTTTTCT +ATGTACTTGGATTGGCTGCAATCATGCAATTGTTTTTCAGCTATTTTGCAGTACATTTTATTAGTAATTC +TTGGCTTATGTGGTTAATAATTAATCTTGTACAAATGGCCCCGATTTCAGCTATGGTTAGAATGTACATC +TTCTTTGCATCATTTTATTATGTATGGAAAAGTTATGTGCATGTTGTAGACGGTTGTAATTCATCAACTT +GTATGATGTGTTACAAACGTAATAGAGCAACAAGAGTCGAATGTACAACTATTGTTAATGGTGTTAGAAG +GTCCTTTTATGTCTATGCTAATGGAGGTAAAGGCTTTTGCAAACTACACAATTGGAATTGTGTTAATTGT +GATACATTCTGTGCTGGTAGTACATTTATTAGTGATGAAGTTGCGAGAGACTTGTCACTACAGTTTAAAA +GACCAATAAATCCTACTGACCAGTCTTCTTACATCGTTGATAGTGTTACAGTGAAGAATGGTTCCATCCA +TCTTTACTTTGATAAAGCTGGTCAAAAGACTTATGAAAGACATTCTCTCTCTCATTTTGTTAACTTAGAC +AACCTGAGAGCTAATAACACTAAAGGTTCATTGCCTATTAATGTTATAGTTTTTGATGGTAAATCAAAAT +GTGAAGAATCATCTGCAAAATCAGCGTCTGTTTACTACAGTCAGCTTATGTGTCAACCTATACTGTTACT +AGATCAGGCATTAGTGTCTGATGTTGGTGATAGTGCGGAAGTTGCAGTTAAAATGTTTGATGCTTACGTT +AATACGTTTTCATCAACTTTTAACGTACCAATGGAAAAACTCAAAACACTAGTTGCAACTGCAGAAGCTG +AACTTGCAAAGAATGTGTCCTTAGACAATGTCTTATCTACTTTTATTTCAGCAGCTCGGCAAGGGTTTGT +TGATTCAGATGTAGAAACTAAAGATGTTGTTGAATGTCTTAAATTGTCACATCAATCTGACATAGAAGTT +ACTGGCGATAGTTGTAATAACTATATGCTCACCTATAACAAAGTTGAAAACATGACACCCCGTGACCTTG +GTGCTTGTATTGACTGTAGTGCGCGTCATATTAATGCGCAGGTAGCAAAAAGTCACAACATTGCTTTGAT +ATGGAACGTTAAAGATTTCATGTCATTGTCTGAACAACTACGAAAACAAATACGTAGTGCTGCTAAAAAG +AATAACTTACCTTTTAAGTTGACATGTGCAACTACTAGACAAGTTGTTAATGTTGTAACAACAAAGATAG +CACTTAAGGGTGGTAAAATTGTTAATAATTGGTTGAAGCAGTTAATTAAAGTTACACTTGTGTTCCTTTT +TGTTGCTGCTATTTTCTATTTAATAACACCTGTTCATGTCATGTCTAAACATACTGACTTTTCAAGTGAA +ATCATAGGATACAAGGCTATTGATGGTGGTGTCACTCGTGACATAGCATCTACAGATACTTGTTTTGCTA +ACAAACATGCTGATTTTGACACATGGTTTAGCCAGCGTGGTGGTAGTTATACTAATGACAAAGCTTGCCC +ATTGATTGCTGCAGTCATAACAAGAGAAGTGGGTTTTGTCGTGCCTGGTTTGCCTGGCACGATATTACGC +ACAACTAATGGTGACTTTTTGCATTTCTTACCTAGAGTTTTTAGTGCAGTTGGTAACATCTGTTACACAC +CATCAAAACTTATAGAGTACACTGACTTTGCAACATCAGCTTGTGTTTTGGCTGCTGAATGTACAATTTT +TAAAGATGCTTCTGGTAAGCCAGTACCATATTGTTATGATACCAATGTACTAGAAGGTTCTGTTGCTTAT +GAAAGTTTACGCCCTGACACACGTTATGTGCTCATGGATGGCTCTATTATTCAATTTCCTAACACCTACC +TTGAAGGTTCTGTTAGAGTGGTAACAACTTTTGATTCTGAGTACTGTAGGCACGGCACTTGTGAAAGATC +AGAAGCTGGTGTTTGTGTATCTACTAGTGGTAGATGGGTACTTAACAATGATTATTACAGATCTTTACCA +GGAGTTTTCTGTGGTGTAGATGCTGTAAATTTACTTACTAATATGTTTACACCACTAATTCAACCTATTG +GTGCTTTGGACATATCAGCATCTATAGTAGCTGGTGGTATTGTAGCTATCGTAGTAACATGCCTTGCCTA +CTATTTTATGAGGTTTAGAAGAGCTTTTGGTGAATACAGTCATGTAGTTGCCTTTAATACTTTACTATTC +CTTATGTCATTCACTGTACTCTGTTTAACACCAGTTTACTCATTCTTACCTGGTGTTTATTCTGTTATTT +ACTTGTACTTGACATTTTATCTTACTAATGATGTTTCTTTTTTAGCACATATTCAGTGGATGGTTATGTT +CACACCTTTAGTACCTTTCTGGATAACAATTGCTTATATCATTTGTATTTCCACAAAGCATTTCTATTGG +TTCTTTAGTAATTACCTAAAGAGACGTGTAGTCTTTAATGGTGTTTCCTTTAGTACTTTTGAAGAAGCTG +CGCTGTGCACCTTTTTGTTAAATAAAGAAATGTATCTAAAGTTGCGTAGTGATGTGCTATTACCTCTTAC +GCAATATAATAGATACTTAGCTCTTTATAATAAGTACAAGTATTTTAGTGGAGCAATGGATACAACTAGC +TACAGAGAAGCTGCTTGTTGTCATCTCGCAAAGGCTCTCAATGACTTCAGTAACTCAGGTTCTGATGTTC +TTTACCAACCACCACAAACCTCTATCACCTCAGCTGTTTTGCAGAGTGGTTTTAGAAAAATGGCATTCCC +ATCTGGTAAAGTTGAGGGTTGTATGGTACAAGTAACTTGTGGTACAACTACACTTAACGGTCTTTGGCTT +GATGACGTAGTTTACTGTCCAAGACATGTGATCTGCACCTCTGAAGACATGCTTAACCCTAATTATGAAG +ATTTACTCATTCGTAAGTCTAATCATAATTTCTTGGTACAGGCTGGTAATGTTCAACTCAGGGTTATTGG +ACATTCTATGCAAAATTGTGTACTTAAGCTTAAGGTTGATACAGCCAATCCTAAGACACCTAAGTATAAG +TTTGTTCGCATTCAACCAGGACAGACTTTTTCAGTGTTAGCTTGTTACAATGGTTCACCATCTGGTGTTT +ACCAATGTGCTATGAGGCCCAATTTCACTATTAAGGGTTCATTCCTTAATGGTTCATGTGGTAGTGTTGG +TTTTAACATAGATTATGACTGTGTCTCTTTTTGTTACATGCACCATATGGAATTACCAACTGGAGTTCAT +GCTGGCACAGACTTAGAAGGTAACTTTTATGGACCTTTTGTTGACAGGCAAACAGCACAAGCAGCTGGTA +CGGACACAACTATTACAGTTAATGTTTTAGCTTGGTTGTACGCTGCTGTTATAAATGGAGACAGGTGGTT +TCTCAATCGATTTACCACAACTCTTAATGACTTTAACCTTGTGGCTATGAAGTACAATTATGAACCTCTA +ACACAAGACCATGTTGACATACTAGGACCTCTTTCTGCTCAAACTGGAATTGCCGTTTTAGATATGTGTG +CTTCATTAAAAGAATTACTGCAAAATGGTATGAATGGACGTACCATATTGGGTAGTGCTTTATTAGAAGA +TGAATTTACACCTTTTGATGTTGTTAGACAATGCTCAGGTGTTACTTTCCAAAGTGCAGTGAAAAGAACA +ATCAAGGGTACACACCACTGGTTGTTACTCACAATTTTGACTTCACTTTTAGTTTTAGTCCAGAGTACTC +AATGGTCTTTGTTCTTTTTTTTGTATGAAAATGCCTTTTTACCTTTTGCTATGGGTATTATTGCTATGTC +TGCTTTTGCAATGATGTTTGTCAAACATAAGCATGCATTTCTCTGTTTGTTTTTGTTACCTTCTCTTGCC +ACTGTAGCTTATTTTAATATGGTCTATATGCCTGCTAGTTGGGTGATGCGTATTATGACATGGTTGGATA +TGGTTGATACTAGTTTGTCTGGTTTTAAGCTAAAAGACTGTGTTATGTATGCATCAGCTGTAGTGTTACT +AATCCTTATGACAGCAAGAACTGTGTATGATGATGGTGCTAGGAGAGTGTGGACACTTATGAATGTCTTG +ACACTCGTTTATAAAGTTTATTATGGTAATGCTTTAGATCAAGCCATTTCCATGTGGGCTCTTATAATCT +CTGTTACTTCTAACTACTCAGGTGTAGTTACAACTGTCATGTTTTTGGCCAGAGGTATTGTTTTTATGTG +TGTTGAGTATTGCCCTATTTTCTTCATAACTGGTAATACACTTCAGTGTATAATGCTAGTTTATTGTTTC +TTAGGCTATTTTTGTACTTGTTACTTTGGCCTCTTTTGTTTACTCAACCGCTACTTTAGACTGACTCTTG +GTGTTTATGATTACTTAGTTTCTACACAGGAGTTTAGATATATGAATTCACAGGGACTACTCCCACCCAA +GAATAGCATAGATGCCTTCAAACTCAACATTAAATTGTTGGGTGTTGGTGGCAAACCTTGTATCAAAGTA +GCCACTGTACAGTCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAAC +TCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAA +AGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTA +GACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAAGCTATAGCCTCAGAGTTTA +GTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGA +TTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCA +GCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTG +AGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAA +TGATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACA +ACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACAT +TTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAG +TGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCT +GCTGTCAAATTACAGAATAATGAGCTTAGTCCTGTTGCACTACGACAGATGTCTTGTGCTGCCGGTACTA +CACAAACTGCTTGCACTGATGACAATGCGTTAGCTTACTACAACACAACAAAGGGAGGTAGGTTTGTACT +TGCACTGTTATCCGATTTACAGGATTTGAAATGGGCTAGATTCCCTAAGAGTGATGGAACTGGTACTATC +TATACAGAACTGGAACCACCTTGTAGGTTTGTTACAGACACACCTAAAGGTCCTAAAGTGAAGTATTTAT +ACTTTATTAAAGGATTAAACAACCTAAATAGAGGTATGGTACTTGGTAGTTTAGCTGCCACAGTACGTCT +ACAAGCTGGTAATGCAACAGAAGTGCCTGCCAATTCAACTGTATTATCTTTCTGTGCTTTTGCTGTAGAT +GCTGCTAAAGCTTACAAAGATTATCTAGCTAGTGGGGGACAACCAATCACTAATTGTGTTAAGATGTTGT +GTACACACACTGGTACTGGTCAGGCAATAACAGTTACACCGGAAGCCAATATGGATCAAGAATCCTTTGG +TGGTGCATCGTGTTGTCTGTACTGCCGTTGCCACATAGATCATCCAAATCCTAAAGGATTTTGTGACTTA +AAAGGTAAGTATGTACAAATACCTACAACTTGTGCTAATGACCCTGTGGGTTTTACACTTAAAAACACAG +TCTGTACCGTCTGCGGTATGTGGAAAGGTTATGGCTGTAGTTGTGATCAACTCCGCGAACCCATGCTTCA +GTCAGCTGATGCACAATCGTTTTTAAACGGGTTTGCGGTGTAAGTGCAGCCCGTCTTACACCGTGCGGCA +CAGGCACTAGTACTGATGTCGTATACAGGGCTTTTGACATCTACAATGATAAAGTAGCTGGTTTTGCTAA +ATTCCTAAAAACTAATTGTTGTCGCTTCCAAGAAAAGGACGAAGATGACAATTTAATTGATTCTTACTTT +GTAGTTAAGAGACACACTTTCTCTAACTACCAACATGAAGAAACAATTTATAATTTACTTAAGGATTGTC +CAGCTGTTGCTAAACATGACTTCTTTAAGTTTAGAATAGACGGTGACATGGTACCACATATATCACGTCA +ACGTCTTACTAAATACACAATGGCAGACCTCGTCTATGCTTTAAGGCATTTTGATGAAGGTAATTGTGAC +ACATTAAAAGAAATACTTGTCACATACAATTGTTGTGATGATGATTATTTCAATAAAAAGGACTGGTATG +ATTTTGTAGAAAACCCAGATATATTACGCGTATACGCCAACTTAGGTGAACGTGTACGCCAAGCTTTGTT +AAAAACAGTACAATTCTGTGATGCCATGCGAAATGCTGGTATTGTTGGTGTACTGACATTAGATAATCAA +GATCTCAATGGTAACTGGTATGATTTCGGTGATTTCATACAAACCACGCCAGGTAGTGGAGTTCCTGTTG +TAGATTCTTATTATTCATTGTTAATGCCTATATTAACCTTGACCAGGGCTTTAACTGCAGAGTCACATGT +TGACACTGACTTAACAAAGCCTTACATTAAGTGGGATTTGTTAAAATATGACTTCACGGAAGAGAGGTTA +AAACTCTTTGACCGTTATTTTAAATATTGGGATCAGACATACCACCCAAATTGTGTTAACTGTTTGGATG +ACAGATGCATTCTGCATTGTGCAAACTTTAATGTTTTATTCTCTACAGTGTTCCCACCTACAAGTTTTGG +ACCACTAGTGAGAAAAATATTTGTTGATGGTGTTCCATTTGTAGTTTCAACTGGATACCACTTCAGAGAG +CTAGGTGTTGTACATAATCAGGATGTAAACTTACATAGCTCTAGACTTAGTTTTAAGGAATTACTTGTGT +ATGCTGCTGACCCTGCTATGCACGCTGCTTCTGGTAATCTATTACTAGATAAACGCACTACGTGCTTTTC +AGTAGCTGCACTTACTAACAATGTTGCTTTTCAAACTGTCAAACCCGGTAATTTTAACAAAGACTTCTAT +GACTTTGCTGTGTCTAAGGGTTTCTTTAAGGAAGGAAGTTCTGTTGAATTAAAACACTTCTTCTTTGCTC +AGGATGGTAATGCTGCTATCAGCGATTATGACTACTATCGTTATAATCTACCAACAATGTGTGATATCAG +ACAACTACTATTTGTAGTTGAAGTTGTTGATAAGTACTTTGATTGTTACGATGGTGGCTGTATTAATGCT +AACCAAGTCATCGTCAACAACCTAGACAAATCAGCTGGTTTTCCATTTAATAAATGGGGTAAGGCTAGAC +TTTATTATGATTCAATGAGTTATGAGGATCAAGATGCACTTTTCGCATATACAAAACGTAATGTCATCCC +TACTATAACTCAAATGAATCTTAAGTATGCCATTAGTGCAAAGAATAGAGCTCGCACCGTAGCTGGTGTC +TCTATCTGTAGTACTATGACCAATAGACAGTTTCATCAAAAATTATTGAAATCAATAGCCGCCACTAGAG +GAGCTACTGTAGTAATTGGAACAAGCAAATTCTATGGTGGTTGGCACAACATGTTAAAAACTGTTTATAG +TGATGTAGAAAACCCTCACCTTATGGGTTGGGATTATCCTAAATGTGATAGAGCCATGCCTAACATGCTT +AGAATTATGGCCTCACTTGTTCTTGCTCGCAAACATACAACGTGTTGTAGCTTGTCACACCGTTTCTATA +GATTAGCTAATGAGTGTGCTCAAGTATTGAGTGAAATGGTCATGTGTGGCGGTTCACTATATGTTAAACC +AGGTGGAACCTCATCAGGAGATGCCACAACTGCTTATGCTAATAGTGTTTTTAACATTTGTCAAGCTGTC +ACGGCCAATGTTAATGCACTTTTATCTACTGATGGTAACAAAATTGCCGATAAGTATGTCCGCAATTTAC +AACACAGACTTTATGAGTGTCTCTATAGAAATAGAGATGTTGACACAGACTTTGTGAATGAGTTTTACGC +ATATTTGCGTAAACATTTCTCAATGATGATACTCTCTGACGATGCTGTTGTGTGTTTCAATAGCACTTAT +GCATCTCAAGGTCTAGTGGCTAGCATAAAGAACTTTAAGTCAGTTCTTTATTATCAAAACAATGTTTTTA +TGTCTGAAGCAAAATGTTGGACTGAGACTGACCTTACTAAAGGACCTCATGAATTTTGCTCTCAACATAC +AATGCTAGTTAAACAGGGTGATGATTATGTGTACCTTCCTTACCCAGATCCATCAAGAATCCTAGGGGCC +GGCTGTTTTGTAGATGATATCGTAAAAACAGATGGTACACTTATGATTGAACGGTTCGTGTCTTTAGCTA +TAGATGCTTACCCACTTACTAAACATCCTAATCAGGAGTATGCTGATGTCTTTCATTTGTACTTACAATA +CATAAGAAAGCTACATGATGAGTTAACAGGACACATGTTAGACATGTATTCTGTTATGCTTACTAATGAT +AACACTTCAAGGTATTGGGAACCTGAGTTTTATGAGGCTATGTACACACCGCATACAGTCTTACAGGCTG +TTGGGGCTTGTGTTCTTTGCAATTCACAGACTTCATTAAGATGTGGTGCTTGCATACGTAGACCATTCTT +ATGTTGTAAATGCTGTTACGACCATGTCATATCAACATCACATAAATTAGTCTTGTCTGTTAATCCGTAT +GTTTGCAATGCTCCAGGTTGTGATGTCACAGATGTGACTCAACTTTACTTAGGAGGTATGAGCTATTATT +GTAAATCACATAAACCACCCATTAGTTTTCCATTGTGTGCTAATGGACAAGTTTTTGGTTTATATAAAAA +TACATGTGTTGGTAGCGATAATGTTACTGACTTTAATGCAATTGCAACATGTGACTGGACAAATGCTGGT +GATTACATTTTAGCTAACACCTGTACTGAAAGACTCAAGCTTTTTGCAGCAGAAACGCTCAAAGCTACTG +AGGAGACATTTAAACTGTCTTATGGTATTGCTACTGTACGTGAAGTGCTGTCTGACAGAGAATTACATCT +TTCATGGGAAGTTGGTAAACCTAGACCACCACTTAACCGAAATTATGTCTTTACTGGTTATCGTGTAACT +AAAAACAGTAAAGTACAAATAGGAGAGTACACCTTTGAAAAAGGTGACTATGGTGATGCTGTTGTTTACC +GAGGTACAACAACTTACAAATTAAATGTTGGTGATTATTTTGTGCTGACATCACATACAGTAATGCCATT +AAGTGCACCTACACTAGTGCCACAAGAGCACTATGTTAGAATTACTGGCTTATACCCAACACTCAATATC +TCAGATGAGTTTTCTAGCAATGTTGCAAATTATCAAAAGGTTGGTATGCAAAAGTATTCTACACTCCAGG +GACCACCTGGTACTGGTAAGAGTCATTTTGCTATTGGCCTAGCTCTCTACTACCCTTCTGCTCGCATAGT +GTATACAGCTTGCTCTCATGCCGCTGTTGATGCACTATGTGAGAAGGCATTAAAATATTTGCCTATAGAT +AAATGTAGTAGAATTATACCTGCACGTGCTCGTGTAGAGTGTTTTGATAAATTCAAAGTGAATTCAACAT +TAGAACAGTATGTCTTTTGTACTGTAAATGCATTGCCTGAGACGACAGCAGATATAGTTGTCTTTGATGA +AATTTCAATGGCCACAAATTATGATTTGAGTGTTGTCAATGCCAGATTACGTGCTAAGCACTATGTGTAC +ATTGGCGACCCTGCTCAATTACCTGCACCACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATT +TCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCC +TGCTGAAATTGTTGACACTGTGAGTGCTTTGGTTTATGATAATAAGCTTAAAGCACATAAAGACAAATCA +GCTCAATGCTTTAAAATGTTTTATAAGGGTGTTATCACGCATGATGTTTCATCTGCAATTAACAGGCCAC +AAATAGGCGTGGTAAGAGAATTCCTTACACGTAACCCTGCTTGGAGAAAAGCTGTCTTTATTTCACCTTA +TAATTCACAGAATGCTGTAGCCTCAAAGATTTTGGGACTACCAACTCAAACTGTTGATTCATCACAGGGC +TCAGAATATGACTATGTCATATTCACTCAAACCACTGAAACAGCTCACTCTTGTAATGTAAACAGATTTA +ATGTTGCTATTACCAGAGCAAAAGTAGGCATACTTTGCATAATGTCTGATAGAGACCTTTATGACAAGTT +GCAATTTACAAGTCTTGAAATTCCACGTAGGAATGTGGCAACTTTACAAGCTGAAAATGTAACAGGACTC +TTTAAAGATTGTAGTAAGGTAATCACTGGGTTACATCCTACACAGGCACCTACACACCTCAGTGTTGACA +CTAAATTCAAAACTGAAGGTTTATGTGTTGACATACCTGGCATACCTAAGGACATGACCTATAGAAGACT +CATCTCTATGATGGGTTTTAAAATGAATTATCAAGTTAATGGTTACCCTAACATGTTTATCACCCGCGAA +GAAGCTATAAGACATGTACGTGCATGGATTGGCTTCGATGTCGAGGGGTGTCATGCTACTAGAGAAGCTG +TTGGTACCAATTTACCTTTACAGCTAGGTTTTTCTACAGGTGTTAACCTAGTTGCTGTACCTACAGGTTA +TGTTGATACACCTAATAATACAGATTTTTCCAGAGTTAGTGCTAAACCACCGCCTGGAGATCAATTTAAA +CACCTCATACCACTTATGTACAAAGGACTTCCTTGGAATGTAGTGCGTATAAAGATTGTACAAATGTTAA +GTGACACACTTAAAAATCTCTCTGACAGAGTCGTATTTGTCTTATGGGCACATGGCTTTGAGTTGACATC +TATGAAGTATTTTGTGAAAATAGGACCTGAGCGCACCTGTTGTCTATGTGATAGACGTGCCACATGCTTT +TCCACTGCTTCAGACACTTATGCCTGTTGGCATCATTCTATTGGATTTGATTACGTCTATAATCCGTTTA +TGATTGATGTTCAACAATGGGGTTTTACAGGTAACCTACAAAGCAACCATGATCTGTATTGTCAAGTCCA +TGGTAATGCACATGTAGCTAGTTGTGATGCAATCATGACTAGGTGTCTAGCTGTCCACGAGTGCTTTGTT +AAGCGTGTTGACTGGACTATTGAATATCCTATAATTGGTGATGAACTGAAGATTAATGCGGCTTGTAGAA +AGGTTCAACACATGGTTGTTAAAGCTGCATTATTAGCAGACAAATTCCCAGTTCTTCACGACATTGGTAA +CCCTAAAGCTATTAAGTGTGTACCTCAAGCTGATGTAGAATGGAAGTTCTATGATGCACAGCCTTGTAGT +GACAAAGCTTATAAAATAGAAGAATTATTCTATTCTTATGCCACACATTCTGACAAATTCACAGATGGTG +TATGCCTATTTTGGAATTGCAATGTCGATAGATATCCTGCTAATTCCATTGTTTGTAGATTTGACACTAG +AGTGCTATCTAACCTTAACTTGCCTGGTTGTGATGGTGGCAGTTTGTATGTAAATAAACATGCATTCCAC +ACACCAGCTTTTGATAAAAGTGCTTTTGTTAATTTAAAACAATTACCATTTTTCTATTACTCTGACAGTC +CATGTGAGTCTCATGGAAAACAAGTAGTGTCAGATATAGATTATGTACCACTAAAGTCTGCTACGTGTAT +AACACGTTGCAATTTAGGTGGTGCTGTCTGTAGACATCATGCTAATGAGTACAGATTGTATCTCGATGCT +TATAACATGATGATCTCAGCTGGCTTTAGCTTGTGGGTTTACAAACAATTTGATACTTATAACCTCTGGA +ACACTTTTACAAGACTTCAGAGTTTAGAAAATGTGGCTTTTAATGTTGTAAATAAGGGACACTTTGATGG +ACAACAGGGTGAAGTACCAGTTTCTATCATTAATAACACTGTTTACACAAAAGTTGATGGTGTTGATGTA +GAATTGTTTGAAAATAAAACAACATTACCTGTTAATGTAGCATTTGAGCTTTGGGCTAAGCGCAACATTA +AACCAGTACCAGAGGTGAAAATACTCAATAATTTGGGTGTGGACATTGCTGCTAATACTGTGATCTGGGA +CTACAAAAGAGATGCTCCAGCACATATATCTACTATTGGTGTTTGTTCTATGACTGACATAGCCAAGAAA +CCAACTGAAACGATTTGTGCACCACTCACTGTCTTTTTTGATGGTAGAGTTGATGGTCAAGTAGACTTAT +TTAGAAATGCCCGTAATGGTGTTCTTATTACAGAAGGTAGTGTTAAAGGTTTACAACCATCTGTAGGTCC +CAAACAAGCTAGTCTTAATGGAGTCACATTAATTGGAGAAGCCGTAAAAACACAGTTCAATTATTATAAG +AAAGTTGATGGTGTTGTCCAACAATTACCTGAAACTTACTTTACTCAGAGTAGAAATTTACAAGAATTTA +AACCCAGGAGTCAAATGGAAATTGATTTCTTAGAATTAGCTATGGATGAATTCATTGAACGGTATAAATT +AGAAGGCTATGCCTTCGAACATATCGTTTATGGAGATTTTAGTCATAGTCAGTTAGGTGGTTTACATCTA +CTGATTGGACTAGCTAAACGTTTTAAGGAATCACCTTTTGAATTAGAAGATTTTATTCCTATGGACAGTA +CAGTTAAAAACTATTTCATAACAGATGCGCAAACAGGTTCATCTAAGTGTGTGTGTTCTGTTATTGATTT +ATTACTTGATGATTTTGTTGAAATAATAAAATCCCAAGATTTATCTGTAGTTTCTAAGGTTGTCAAAGTG +ACTATTGACTATACAGAAATTTCATTTATGCTTTGGTGTAAAGATGGCCATGTAGAAACATTTTACCCAA +AATTACAATCTAGTCAAGCGTGGCAACCGGGTGTTGCTATGCCTAATCTTTACAAAATGCAAAGAATGCT +ATTAGAAAAGTGTGACCTTCAAAATTATGGTGATAGTGCAACATTACCTAAAGGCATAATGATGAATGTC +GCAAAATATACTCAACTGTGTCAATATTTAAACACATTAACATTAGCTGTACCCTATAATATGAGAGTTA +TACATTTTGGTGCTGGTTCTGATAAAGGAGTTGCACCAGGTACAGCTGTTTTAAGACAGTGGTTGCCTAC +GGGTACGCTGCTTGTCGATTCAGATCTTAATGACTTTGTCTCTGATGCAGATTCAACTTTGATTGGTGAT +TGTGCAACTGTACATACAGCTAATAAATGGGATCTCATTATTAGTGATATGTACGACCCTAAGACTAAAA +ATGTTACAAAAGAAAATGACTCTAAAGAGGGTTTTTTCACTTACATTTGTGGGTTTATACAACAAAAGCT +AGCTCTTGGAGGTTCCGTGGCTATAAAGATAACAGAACATTCTTGGAATGCTGATCTTTATAAGCTCATG +GGACACTTCGCATGGTGGACAGCCTTTGTTACTAATGTGAATGCGTCATCATCTGAAGCATTTTTAATTG +GATGTAATTATCTTGGCAAACCACGCGAACAAATAGATGGTTATGTCATGCATGCAAATTACATATTTTG +GAGGAATACAAATCCAATTCAGTTGTCTTCCTATTCTTTATTTGACATGAGTAAATTTCCCCTTAAATTA +AGGGGTACTGCTGTTATGTCTTTAAAAGAAGGTCAAATCAATGATATGATTTTATCTCTTCTTAGTAAAG +GTAGACTTATAATTAGAGAAAACAACAGAGTTGTTATTTCTAGTGATGTTCTTGTTAACAACTAAACGAA +CAATGTTTGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACCAGAACTCA +ATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGACAAAGTTTTCAGATCCTCA +GTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCCAATGTTACTTGGTTCCATGCTATACATG +TCTCTGGGACCAATGGTACTAAGAGGTTTGATAACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGC +TTCCACTGAGAAGTCTAACATAATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCC +CTACTTATTGTTAATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATGATCCAT +TTTTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTATTCTAGTGC +GAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAAGGAAAACAGGGTAATTTC +AAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTATTTTAAAATATATTCTAAGCACACGCCTA +TTAATTTAGTGCGTGATCTCCCTCAGGGTTTTTCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTAT +TAACATCACTAGGTTTCAAACTTTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCA +GGTTGGACAGCTGGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATA +ATGAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAGTGTACGTT +GAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTCCAACCAACAGAATCTATT +GTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAAGTTTTTAACGCCACCAGATTTGCATCTG +TTTATGCTTGGAACAGGAAGAGAATCAGCAACTGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATC +ATTTTCCACTTTTAAGTGTTATGGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTAT +GCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTG +ATTATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAATCTTGATTC +TAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAATCTCAAACCTTTTGAGAGA +GATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGTAATGGTGTTGAAGGTTTTAATTGTTACT +TTCCTTTACAATCATATGGTTTCCAACCCACTAATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACT +TTCTTTTGAACTTCTACATGCACCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAAC +AAATGTGTCAATTTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTC +TGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAGACACTTGA +GATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCAGGAACAAATACTTCTAAC +CAGGTTGCTGTTCTTTATCAGGATGTTAACTGCACAGAAGTCCCTGTTGCTATTCATGCAGATCAACTTA +CTCCTACTTGGCGTGTTTATTCTACAGGTTCTAATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGC +TGAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACT +CAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTG +GTGCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATTAGTGTTAC +CACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATGTACATTTGTGGTGATTCA +ACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGTACACAATTAAACCGTGCTTTAACTGGAA +TAGCTGTTGAACAAGACAAAAACACCCAAGAAGTTTTTGCACAAGTCAAACAAATTTACAAAACACCACC +AATTAAAGATTTTGGTGGTTTTAATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCA +TTTATTGAAGATCTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATT +GCCTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTTTTGCCACC +TTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGTACAATCACTTCTGGTTGG +ACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATGCAAATGGCTTATAGGTTTAATGGTATTG +GAGTTACACAGAATGTTCTCTATGAGAACCAAAAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAA +AATTCAAGACTCACTTTCTTCCACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCA +CAAGCTTTAAACACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATA +TCCTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGACTTCAAAG +TTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCTTCTGCTAATCTTGCTGCT +ACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTTGATTTTTGTGGAAAGGGCTATCATCTTA +TGTCCTTCCCTCAGTCAGCACCTCATGGTGTAGTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAA +GAACTTCACAACTGCTCCTGCCATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTT +TCAAATGGCACACACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACA +CATTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCTTTGCAACC +TGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACATCACCAGATGTTGATTTA +GGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAAAAAGAAATTGACCGCCTCAATGAGGTTG +CCAAGAATTTAAATGAATCTCTCATCGATCTCCAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCC +ATGGTACATTTGGCTAGGTTTTATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGT +ATGACCAGTTGCTGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACG +ACTCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACATAAACGAACTTATGGATTTGTTTATGAGA +ATCTTCACAATTGGAACTGTAACTTTGAAGCAAGGTGAAATCAAGGATGCTACTCCTTCAGATTTTGTTC +GCGCTACTGCAACGATACCGATACAAGCCTCACTCCCTTTCGGATGGCTTATTGTTGGCGTTGCACTTCT +TGCTGTTTTTCAGAGCGCTTCCAAAATCATAACCCTCAAAAAGAGATGGCAACTAGCACTCTCCAAGGGT +GTTCACTTTGTTTGCAACTTGCTGTTGTTGTTTGTAACAGTTTACTCACACCTTTTGCTCGTTGCTGCTG +GCCTTGAAGCCCCTTTTCTCTATCTTTATGCTTTAGTCTACTTCTTGCAGAGTATAAACTTTGTAAGAAT +AATAATGAGGCTTTGGCTTTGCTGGAAATGCCGTTCCAAAAACCCATTACTTTATGATGCCAACTATTTT +CTTTGCTGGCATACTAATTGTTACGACTATTGTATACCTTACAATAGTGTAACTTCTTCAATTGTCATTA +CTTCAGGTGATGGCACAACAAGTCCTATTTCTGAACATGACTACCAGATTGGTGGTTATACTGAAAAATG +GGAATCTGGAGTAAAAGACTGTGTTGTATTACACAGTTACTTCACTTCAGACTATTACCAGCTGTACTCA +ACTCAATTGAGTACAGACACTGGTGTTGAACATGTTACCTTCTTCATCTACAATAAAATTGTTGATGAGC +CTGAAGAACATGTCCAAATTCACACAATCGACGGTTCATCCGGAGTTGTTAATCCAGTAATGGAACCAAT +TTATGATGAACCGACGACGACTACTAGCGTGCCTTTGTAAGCACAAGCTGATGAGTACGAACTTATGTAC +TCATTCGTTTCGGAAGAGACAGGTACGTTAATAGTTAATAGCGTACTTCTTTTTCTTGCTTTCGTGGTAT +TCTTGCTAGTTACACTAGCCATCCTTACTGCGCTTCGATTGTGTGCGTACTGCTGCAATATTGTTAACGT +GAGTCTTGTAAAACCTTCTTTTTACGTTTACTCTCGTGTTAAAAATCTGAATTCTTCTAGAGTTCCTGAT +CTTCTGGTCTAAACGAACTAAATATTATATTAGTTTTTCTGTTTGGAACTTTAATTTTAGCCATGGCAGA +TTCCAACGGTACTATTACCGTTGAAGAGCTTAAAAAGCTCCTTGAACAATGGAACCTAGTAATAGGTTTC +CTATTCCTTACATGGATTTGTCTTCTACAATTTGCCTATGCCAACAGGAATAGGTTTTTGTATATAATTA +AGTTAATTTTCCTCTGGCTGTTATGGCCAGTAACTTTAGCTTGTTTTGTGCTTGCTGCTGTTTACAGAAT +AAATTGGATCACCGGTGGAATTGCTATCGCAATGGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTC +ATTGCTTCTTTCAGACTGTTTGCGCGTACGCGTTCCATGTGGTCATTCAATCCAGAAACTAACATTCTTC +TCAACGTGCCACTCCATGGCACTATTCTGACCAGACCGCTTCTAGAAAGTGAACTCGTAATCGGAGCTGT +GATCCTTCGTGGACATCTTCGTATTGCTGGACACCATCTAGGACGCTGTGACATCAAGGACCTGCCTAAA +GAAATCACTGTTGCTACATCACGAACGCTTTCTTATTACAAATTGGGAGCTTCGCAGCGTGTAGCAGGTG +ACTCAGGTTTTGCTGCATACAGTCGCTACAGGATTGGCAACTATAAATTAAACACAGACCATTCCAGTAG +CAGTGACAATATTGCTTTGCTTGTACAGTAAGTGACAACAGATGTTTCATCTCGTTGACTTTCAGGTTAC +TATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATA +AACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAAC +CAATGGAGATTGATTAAACGAACATGAAAATTATTCTTTTCTTGGCACTGATAACACTCGCTACTTGTGA +GCTTTATCACTACCAAGAGTGTGTTAGAGGTACAACAGTACTTTTAAAAGAACCTTGCTCTTCTGGAACA +TACGAGGGCAATTCACCATTTCATCCTCTAGCTGATAACAAATTTGCACTGACTTGCTTTAGCACTCAAT +TTGCTTTTGCTTGTCCTGACGGCGTAAAACACGTCTATCAGTTACGTGCCAGATCAGTTTCACCTAAACT +GTTCATCAGACAAGAGGAAGTTCAAGAACTTTACTCTCCAATTTTTCTTATTGTTGCGGCAATAGTGTTT +ATAACACTTTGCTTCACACTCAAAAGAAAGACAGAATGATTGAACTTTCATTAATTGACTTCTATTTGTG +CTTTTTAGCCTTTCTGCTATTCCTTGTTTTAATTATGCTTATTATCTTTTGGTTCTCACTTGAACTGCAA +GATCATAATGAAACTTGTCACGCCTAAACGAACATGAAATTTCTTGTTTTCTTAGGAATCATCACAACTG +TAGCTGCATTTCACCAAGAATGTAGTTTACAGTCATGTACTCAACATCAACCATATGTAGTTGATGACCC +GTGTCCTATTCACTTCTATTCTAAATGGTATATTAGAGTAGGAGCTAGAAAATCAGCACCTTTAATTGAA +TTGTGCGTGGATGAGGCTGGTTCTAAATCACCCATTCAGTACATCGATATCGGTAATTATACAGTTTCCT +GTTTACCTTTTACAATTAATTGCCAGGAACCTAAATTGGGTAGTCTTGTAGTGCGTTGTTCGTTCTATGA +AGACTTTTTAGAGTATCATGACGTTCGTGTTGTTTTAGATTTCATCTAAACGAACAAACTAAAATGTCTG +ATAATGGACCCCAAAATCAGCGAAATGCACCCCGCATTACGTTTGGTGGACCCTCAGATTCAACTGGCAG +TAACCAGAATGGAGAACGCAGTGGGGCGCGATCAAAACAACGTCGGCCCCAAGGTTTACCCAATAATACT +GCGTCTTGGTTCACCGCTCTCACTCAACATGGCAAGGAAGACCTTAAATTCCCTCGAGGACAAGGCGTTC +CAATTAACACCAATAGCAGTCCAGATGACCAAATTGGCTACTACCGAAGAGCTACCAGACGAATTCGTGG +TGGTGACGGTAAAATGAAAGATCTCAGTCCAAGATGGTATTTCTACTACCTAGGAACTGGGCCAGAAGCT +GGACTTCCCTATGGTGCTAACAAAGACGGCATCATATGGGTTGCAACTGAGGGAGCCTTGAATACACCAA +AAGATCACATTGGCACCCGCAATCCTGCTAACAATGCTGCAATCGTGCTACAACTTCCTCAAGGAACAAC +ATTGCCAAAAGGCTTCTACGCAGAAGGGAGCAGAGGCGGCAGTCAAGCCTCTTCTCGTTCCTCATCACGT +AGTCGCAACAGTTCAAGAAATTCAACTCCAGGCAGCAGTAGGGGAACTTCTCCTGCTAGAATGGCTGGCA +ATGGCGGTGATGCTGCTCTTGCTTTGCTGCTGCTTGACAGATTGAACCAGCTTGAGAGCAAAATGTCTGG +TAAAGGCCAACAACAACAAGGCCAAACTGTCACTAAGAAATCTGCTGCTGAGGCTTCTAAGAAGCCTCGG +CAAAAACGTACTGCCACTAAAGCATACAATGTAACACAAGCTTTCGGCAGACGTGGTCCAGAACAAACCC +AAGGAAATTTTGGGGACCAGGAACTAATCAGACAAGGAACTGATTACAAACATTGGCCGCAAATTGCACA +ATTTGCCCCCAGCGCTTCAGCGTTCTTCGGAATGTCGCGCATTGGCATGGAAGTCACACCTTCGGGAACG +TGGTTGACCTACACAGGTGCCATCAAATTGGATGACAAAGATCCAAATTTCAAAGATCAAGTCATTTTGC +TGAATAAGCATATTGACGCATACAAAACATTCCCACCAACAGAGCCTAAAAAGGACAAAAAGAAGAAGGC +TGATGAAACTCAAGCCTTACCGCAGAGACAGAAGAAACAGCAAACTGTGACTCTTCTTCCTGCTGCAGAT +TTGGATGATTTCTCCAAACAATTGCAACAATCCATGAGCAGTGCTGACTCAACTCAGGCCTAAACTCATG +CAGACCACACAAGGCAGATGGGCTATATAAACGTTTTCGCTTTTCCGTTTACGATATATAGTCTACTCTT +GTGCAGAATGAATTCTCGTAACTACATAGCACAAGTAGATGTAGTTAACTTTAATCTCACATAGCAATCT +TTAATCAGTGTGTAACATTAGGGAGGACTTGAAAGAGCCACCACATTTTCACCGAGGCCACGCGGAGTAC +GATCGAGTGTACAGTGAACAATGCTAGGGAGAGCTGCCTATATGGAAGAGCCCTAATGTGTAAAATTAAT +TTTAGTAGTGCTATCCCCATGTGATTTTAATAGCTTCTTAGGAGAATGACAAAAAAAAAAAAAAAAAAAA +AAAAAAAAAAAAA diff --git a/test/data/different-case/eden.modified.primer.bed b/test/data/different-case/eden.modified.primer.bed new file mode 100644 index 0000000..599a9ac --- /dev/null +++ b/test/data/different-case/eden.modified.primer.bed @@ -0,0 +1,28 @@ +MN908947.3 31 55 SARS2_1_LEFT_1 1 + cCAACCAACTTTCGATCTCTTGTA +MN908947.3 2569 2593 SARS2_1_RIGHT_1 1 - aGCTTCAACAGCTTCACTAGTAGG +MN908947.3 1876 1898 SARS2_2_LEFT_1 2 + tCAGAGGCTGCTCGTGTTGTAC +MN908947.3 4429 4451 SARS2_2_RIGHT_1 2 - tAGTTTCCACACAGACAGGCAT +MN908947.3 4295 4322 SARS2_3_LEFT_1 1 + CAGTGCTTAAAAAGTGTAAAAGTGCCT +MN908947.3 6847 6874 SARS2_3_RIGHT_1 1 - AACAGTATTCTTTGCTATAGTAGTCGG +MN908947.3 6287 6311 SARS2_4_LEFT_1 2 + GGTGTATACGTTGTCTTTGGAGCA +MN908947.3 8828 8852 SARS2_4_RIGHT_1 2 - CCACTTCTCTTGTTATGACTGCAG +MN908947.3 8596 8620 SARS2_5_LEFT_1 1 + CTTGTGTTCCTTTTTGTTGCTGCT +MN908947.3 11049 11075 SARS2_5_RIGHT_1 1 - AGAACAAAGACCATTGAGTACTCTGG +MN908947.3 10363 10385 SARS2_6_LEFT_1 2 + GTTCGCATTCAACCAGGACAGA +MN908947.3 12780 12803 SARS2_6_RIGHT_1 2 - ACCTACCTCCCTTTGTTGTGTTG +MN908947.3 12711 12733 SARS2_7_LEFT_1 1 + ACGACAGATGTCTTGTGCTGCC +MN908947.3 15225 15247 SARS2_7_RIGHT_1 1 - TTAACATGTTGTGCCAACCACC +MN908947.3 14546 14571 SARS2_8_LEFT_1 2 + GGAATTACTTGTGTATGCTGCTGAC +MN908947.3 17131 17153 SARS2_8_RIGHT_1 2 - TACACTATGCGAGCAGAAGGGT +MN908947.3 16847 16872 SARS2_9_LEFT_1 1 + CTATGGTGATGCTGTTGTTTACCGA +MN908947.3 19254 19279 SARS2_9_RIGHT_1 1 - AACCAGGCAAGTTAAGGTTAGATAG +MN908947.3 18897 18919 SARS2_10_LEFT_1 2 + GTTAAGCGTGTTGACTGGACTA +MN908947.3 21428 21456 SARS2_10_RIGHT_1 2 - TTGACCTTCTTTTAAAGACATAACAGCA +MN908947.3 21358 21387 SARS2_11_LEFT_1 1 + CAAATCCAATTCAGTTGTCTTCCTATTCT +MN908947.3 23823 23848 SARS2_11_RIGHT_1 1 - TTGTGTACAAAAACTGCCATATTGC +MN908947.3 23123 23145 SARS2_12_LEFT_1 2 + CAGCAACTGTTTGTGGACCTAA +MN908947.3 25647 25674 SARS2_12_RIGHT_1 2 - AAGGTGTGAGTAAACTGTTACAAACAA +MN908947.3 25602 25624 SARS2_13_LEFT_1 1 + CTAGCACTCTCCAAGGGTGTTC +MN908947.3 28146 28173 SARS2_13_RIGHT_1 1 - TAGGTTCCTGGCAATTAATTGTAAAAG +MN908947.3 27447 27472 SARS2_14_LEFT_1 2 + CACTACCAAGAGTGTGTTAGAGGTA +MN908947.3 29837 29867 SARS2_14_RIGHT_1 2 - ATTCTCCTAAGAAGCTATTAAAATCACATG diff --git a/test/data/many-ref-chroms/info.yml b/test/data/many-ref-chroms/info.yml new file mode 100644 index 0000000..b6d9c00 --- /dev/null +++ b/test/data/many-ref-chroms/info.yml @@ -0,0 +1,11 @@ +schema_version: 1.0.0a +organism: sars-cov-2 +name: artic +amplicon_size: 400 +version: v1.0.0 +developers: +- test +definition_url: https://github.com/pha4ge/primer-schemes/tree/main/sars-cov-2/artic/v4.1 +license: CC-BY-SA-4.0 +primer_checksum: primaschema:bf27195bc23ec05e +reference_checksum: primaschema:1b97591d2f6ab46e diff --git a/test/data/many-ref-chroms/primer.bed b/test/data/many-ref-chroms/primer.bed new file mode 100644 index 0000000..6b3d3b1 --- /dev/null +++ b/test/data/many-ref-chroms/primer.bed @@ -0,0 +1,8 @@ +NC_038235.1 type_a 0 21 scheme-a_1_LEFT_0 1 + ACGCGAAAAAATGCGTACAAC +NC_038235.1 type_a 1213 1233 scheme-a_1_RIGHT_0 1 - TATCTCCTGTGCTCCGTTGG +NC_038235.1 type_a 1123 1144 scheme-a_2_LEFT_0 2 + TGGGGCAAATACAAAGATGGC +NC_038235.1 type_a 2123 2143 scheme-a_2_RIGHT_0 2 - CCCATTATGCCTAGGCCAGC +NC_001781.1 type_b 0 21 scheme-b_1_LEFT_0 1 + ACGCGAAAAAATGCGTACTAC +NC_001781.1 type_b 1213 1233 scheme-b_1_RIGHT_0 1 - TATCTCCTGTACTACGTTGA +NC_001781.1 type_b 1123 1144 scheme-b_2_LEFT_0 2 + TGGGGCAAATACAAAGATGGC +NC_001781.1 type_b 2123 2143 scheme-b_2_RIGHT_0 2 - CCCATTATGCCTAGACCTGC diff --git a/test/data/many-ref-chroms/reference.fasta b/test/data/many-ref-chroms/reference.fasta new file mode 100644 index 0000000..4d65503 --- /dev/null +++ b/test/data/many-ref-chroms/reference.fasta @@ -0,0 +1,439 @@ +>NC_038235.1 Human orthopneumovirus Subgroup A, complete cds +ACGCGAAAAAATGCGTACAACAAACTTGCATAAACCAAAAAAATGGGGCAAATAAGAATTTGATAAGTAC +CACTTAAATTTAACTCCCTTGGTTAGAGATGGGCAGCAATTCATTGAGTATGATAAAAGTTAGATTACAA +AATTTGTTTGACAATGATGAAGTAGCATTGTTAAAAATAACATGCTATACTGATAAATTAATACATTTAA +CTAACGCTTTGGCTAAGGCAGTGATACATACAATCAAATTGAATGGCATTGTGTTTGTGCATGTTATTAC +AAGTAGTGATATTTGCCCTAATAATAATATTGTAGTAAAATCCAATTTCACAACAATGCCAGTACTACAA +AATGGAGGTTATATATGGGAAATGATGGAATTAACACATTGCTCTCAACCTAATGGTCTACTAGATGACA +ATTGTGAAATTAAATTCTCCAAAAAACTAAGTGATTCAACAATGACCAATTATATGAATCAATTATCTGA +ATTACTTGGATTTGATCTTAATCCATAAATTATAATTAATATCAACTAGCAAATCAATGTCACTAACACC +ATTAGTTAATATAAAACTTAACAGAAGACAAAAATGGGGCAAATAAATCAATTCAGCCAACCCAACCATG +GACACAACCCACAATGATAATACACCACAAAGACTGATGATCACAGACATGAGACCGTTGTCACTTGAGA +CCATAATAACATCACTAACCAGAGACATCATAACACACAAATTTATATACTTGATAAATCATGAATGCAT +AGTGAGAAAACTTGATGAAAAACAGGCCACATTTACATTCCTGGTCAACTATGAAATGAAACTATTACAC +AAAGTAGGAAGCACTAAATATAAAAAATATACTGAATACAACACAAAATATGGCACTTTCCCTATGCCAA +TATTCATCAATCATGATGGGTTCTTAGAATGCATTGGCATTAAGCCTACAAAGCATACTCCCATAATATA +CAAGTATGATCTCAATCCATAAATTTCAACACAATATTCACACAATCTAAAACAACAACTCTATGCATAA +CTATACTCCATAGTCCAGATGGAGCCTGAAAATTATAGTAATTTAAAATTAAGGAGAGATATAAGATAGA +AGATGGGGCAAATACAAAGATGGCTCTTAGCAAAGTCAAGTTGAATGATACACTCAACAAAGATCAACTT +CTGTCATCCAGCAAATACACCATCCAACGGAGCACAGGAGATAGTATTGATACTCCTAATTATGATGTGC +AGAAACACATCAATAAGTTATGTGGCATGTTATTAATCACAGAAGATGCTAATCATAAATTCACTGGGTT +AATAGGTATGTTATATGCGATGTCTAGGTTAGGAAGAGAAGACACCATAAAAATACTCAGAGATGCGGGA +TATCATGTAAAAGCAAATGGAGTAGATGTAACAACACATCGTCAAGACATTAATGGAAAAGAAATGAAAT +TTGAAGTGTTAACATTGGCAAGCTTAACAACTGAAATTCAAATCAACATTGAGATAGAATCTAGAAAATC +CTACAAAAAAATGCTAAAAGAAATGGGAGAGGTAGCTCCAGAATACAGGCATGACTCTCCTGATTGTGGG +ATGATAATATTATGTATAGCAGCATTAGTAATAACTAAATTAGCAGCAGGGGACAGATCTGGTCTTACAG +CCGTGATTAGGAGAGCTAATAATGTCCTAAAAAATGAAATGAAACGTTACAAAGGCTTACTACCCAAGGA +CATAGCCAACAGCTTCTATGAAGTGTTTGAAAAACATCCCCACTTTATAGATGTTTTTGTTCATTTTGGT +ATAGCACAATCTTCTACCAGAGGTGGCAGTAGAGTTGAAGGGATTTTTGCAGGATTGTTTATGAATGCCT +ATGGTGCAGGGCAAGTGATGTTACGGTGGGGAGTCTTAGCAAAATCAGTTAAAAATATTATGTTAGGACA +TGCTAGTGTGCAAGCAGAAATGGAACAAGTTGTTGAGGTTTATGAATATGCCCAAAAATTGGGTGGTGAA +GCAGGATTCTACCATATATTGAACAACCCAAAAGCATCATTATTATCTTTGACTCAATTTCCTCACTTCT +CCAGTGTAGTATTAGGCAATGCTGCTGGCCTAGGCATAATGGGAGAGTACAGAGGTACACCGAGGAATCA +AGATCTATATGATGCAGCAAAGGCATATGCTGAACAACTCAAAGAAAATGGTGTGATTAACTACAGTGTA +CTAGACTTGACAGCAGAAGAACTAGAGGCTATCAAACATCAGCTTAATCCAAAAGATAATGATGTAGAGC +TTTGAGTTAATAAAAAATGGGGCAAATAAATCATCATGGAAAAGTTTGCTCCTGAATTCCATGGAGAAGA +TGCAAACAACAGGGCTACTAAATTCCTAGAATCAATAAAGGGCAAATTCACATCACCCAAAGATCCCAAG +AAAAAAGATAGTATCATATCTGTCAACTCAATAGATATAGAAGTAACCAAAGAAAGCCCTATAACATCAA +ATTCAACTATTATCAACCCAACAAATGAGACAGATGATACTGCAGGGAACAAGCCCAATTATCAAAGAAA +ACCTCTAGTAAGTTTCAAAGAAGACCCTACACCAAGTGATAATCCCTTTTCTAAACTATACAAAGAAACC +ATAGAAACATTTGATAACAATGAAGAAGAATCCAGCTATTCATACGAAGAAATAAATGATCAGACAAACG +ATAATATAACAGCAAGATTAGATAGGATTGATGAAAAATTAAGTGAAATACTAGGAATGCTTCACACATT +AGTAGTGGCAAGTGCAGGACCTACATCTGCTCGGGATGGTATAAGAGATGCCATGATTGGTTTAAGAGAA +GAAATGATAGAAAAAATCAGAACTGAAGCATTAATGACCAATGACAGATTAGAAGCTATGGCAAGACTCA +GGAATGAGGAAAGTGAAAAGATGGCAAAAGACACATCAGATGAAGTGTCTCTCAATCCAACATCAGAGAA +ATTGAACAACCTATTGGAAGGGAATGATAGTGACAATGATCTATCACTTGAAGATTTCTGATTAGTTACC +ACTCTTCACATCAACACACAATACCAACAGAAGACCAACAAACTAACCAACCCAATCATCCAACCAAACA +TCCATCCGCCAATCAGCCAAACAGCCAACAAAACAACCAGCCAATCCAAAACTAACCACCCGGAAAAAAT +CTATAATATAGTTACAAAAAAAGGAAAGGGTGGGGCAAATATGGAAACATACGTGAACAAGCTTCACGAA +GGCTCCACATACACAGCTGCTGTTCAATACAATGTCTTAGAAAAAGACGATGACCCTGCATCACTTACAA +TATGGGTGCCCATGTTCCAATCATCTATGCCAGCAGATTTACTTATAAAAGAACTAGCTAATGTCAACAT +ACTAGTGAAACAAATATCCACACCCAAGGGACCTTCACTAAGAGTCATGATAAACTCAAGAAGTGCAGTG +CTAGCACAAATGCCCAGCAAATTTACCATATGCGCTAATGTGTCCTTGGATGAAAGAAGCAAACTAGCAT +ATGATGTAACCACACCCTGTGAAATCAAGGCATGTAGTCTAACATGCCTAAAATCAAAAAATATGTTGAC +TACAGTTAAAGATCTCACTATGAAGACACTCAACCCTACACATGATATTATTGCTTTATGTGAATTTGAA +AACATAGTAACATCAAAAAAAGTCATAATACCAACATACCTAAGATCCATCAGTGTCAGAAATAAAGATC +TGAACACACTTGAAAATATAACAACCACTGAATTCAAAAATGCTATCACAAATGCAAAAATCATCCCTTA +CTCAGGATTACTATTAGTCATCACAGTGACTGACAACAAAGGAGCATTCAAATACATAAAGCCACAAAGT +CAATTCATAGTAGATCTTGGAGCTTACCTAGAAAAAGAAAGTATATATTATGTTACCACAAATTGGAAGC +ACACAGCTACACGATTTGCAATCAAACCCATGGAAGATTAACCTTTTTCCTCTACATCAGTGTGTTAATT +CATACAAACTTTCTACCTACATTCTTCACTTCACCATCACAATCACAAACACTCTGTGGTTCAACCAATC +AAACAAAACTTATCTGAAGTCCCAGATCATCCCAAGTCATTGTTTATCAGATCTAGTACTCAAATAAGTT +AATAAAAAATATACACATGGGGCAAATAATCATTGGAGGAAATCCAACTAATCACAATATCTGTTAACAT +AGACAAGTCCACACACCATACAGAATCAACCAATGGAAAATACATCCATAACAATAGAATTCTCAAGCAA +ATTCTGGCCTTACTTTACACTAATACACATGATCACAACAATAATCTCTTTGCTAATCATAATCTCCATC +ATGATTGCAATACTAAACAAACTTTGTGAATATAACGTATTCCATAACAAAACCTTTGAGTTACCAAGAG +CTCGAGTCAACACATAGCATTCATCAATCCAACAGCCCAAAACAGTAACCTTGCATTTAAAAATGAACAA +CCCCTACCTCTTTACAACACCTCATTAACATCCCACCATGCAAACCACTATCCATACTATAAAGTAGTTA +ATTAAAAATAGTCATAACAATGAACTAGGATATCAAGACTAACAATAACATTGGGGCAAATGCAAACATG +TCCAAAAACAAGGACCAACGCACCGCTAAGACATTAGAAAGGACCTGGGACACTCTCAATCATTTATTAT +TCATATCATCGTGCTTATATAAGTTAAATCTTAAATCTGTAGCACAAATCACATTATCCATTCTGGCAAT +GATAATCTCAACTTCACTTATAATTGCAGCCATCATATTCATAGCCTCGGCAAACCACAAAGTCACACCA +ACAACTGCAATCATACAAGATGCAACAAGCCAGATCAAGAACACAACCCCAACATACCTCACCCAGAATC +CTCAGCTTGGAATCAGTCCCTCTAATCCGTCTGAAATTACATCACAAATCACCACCATACTAGCTTCAAC +AACACCAGGAGTCAAGTCAACCCTGCAATCCACAACAGTCAAGACCAAAAACACAACAACAACTCAAACA +CAACCCAGCAAGCCCACCACAAAACAACGCCAAAACAAACCACCAAGCAAACCCAATAATGATTTTCACT +TTGAAGTGTTCAACTTTGTACCCTGCAGCATATGCAGCAACAATCCAACCTGCTGGGCTATCTGCAAAAG +AATACCAAACAAAAAACCAGGAAAGAAAACCACTACCAAGCCCACAAAAAAACCAACCCTCAAGACAACC +AAAAAAGATCCCAAACCTCAAACCACTAAATCAAAGGAAGTACCCACCACCAAGCCCACAGAAGAGCCAA +CCATCAACACCACCAAAACAAACATCATAACTACACTACTCACCTCCAACACCACAGGAAATCCAGAACT +CACAAGTCAAATGGAAACCTTCCACTCAACTTCCTCCGAAGGCAATCCAAGCCCTTCTCAAGTCTCTACA +ACATCCGAGTACCCATCACAACCTTCATCTCCACCCAACACACCACGCCAGTAGTTACTTAAAAACATAT +TATCACAAAAAGCCATGACCAACTTAAACAGAATCAAAATAAACTCTGGGGCAAATAACAATGGAGTTGC +TAATCCTCAAAGCAAATGCAATTACCACAATCCTCACTGCAGTCACATTTTGTTTTGCTTCTGGTCAAAA +CATCACTGAAGAATTTTATCAATCAACATGCAGTGCAGTTAGCAAAGGCTATCTTAGTGCTCTGAGAACT +GGTTGGTATACCAGTGTTATAACTATAGAATTAAGTAATATCAAGGAAAATAAGTGTAATGGAACAGATG +CTAAGGTAAAATTGATAAAACAAGAATTAGATAAATATAAAAATGCTGTAACAGAATTGCAGTTGCTCAT +GCAAAGCACACCACCAACAAACAATCGAGCCAGAAGAGAACTACCAAGGTTTATGAATTATACACTCAAC +AATGCCAAAAAAACCAATGTAACATTAAGCAAGAAAAGGAAAAGAAGATTTCTTGTTTTTTTGTTAGGTG +TTGGATCTGCAATCGCCAGTGGCGTTGCTGTATCTAAGGTCCTGCACCTAGAAGGGGAAGTGAACAAGAT +CAAAAGTGCTCTACTATCCACAAACAAGGCTCTAGTCAGCTTATCAAATGGAGTTAGTGTCTTAACCAGC +AAAGTGTTAGACCTCAAAAACTATATAGATAAACAATTGTTACCTATTGTGAACAAGCAAAGCTGCAGCA +TATCAAATATAGAAACTGTGATAGAGTTCCAACAAAAGAACAACAGACTACTAGAGATTACCAGGGAATT +TAGTGTTAATGCAGGTGTAACTACACCTGTAAGCACTTACATGTTAACTAATAGTGAATTATTGTCATTA +ATCAATGATATGCCTATAACAAATGATCAGAAAAAGTTAATGTCCAACAATGTTCAAATAGTTAGACAGC +AAAGTTACTCTATCATGTCCATAATAAAAGAGGAAGTCTTAGCATATGTAGTACAATTACCACTATATGG +TGTTATAGATACACCCTGTTGGAAACTACACACATCCCCTCTATGTACAACCAACACAAAAGAAGGGTCC +AACATCTGTTTAACAAGAACTGACAGAGGATGGTACTGTGACAATGCAGGATCAGTATCTTTCTTCCCAC +AAGCTGAAACATGTAAAGTTCAATCAAATCGAGTATTTTGTGACACAATGAACAGTTTAACATTACCAAG +TGAAATAAATCTCTGCAATGTTGACATATTCAACCCCAAATATGATTGTAAAATTATGACTTCAAAAACA +GATGTAAGCAGCTCCGTTATCACATCTCTAGGAGCCATTGTGTCATGCTATGGCAAAACTAAATGTACAG +CATCCAATAAAAATCGTGGAATCATAAAGACATTTTCTAACGGGTGCGATTATGTATCAAATAAAGGGAT +GGACACTGTGTCTGTAGGTAACACATTATATTATGTAAATAAGCAAGAAGGTAAAAGTCTCTATGTAAAA +GGTGAACCAATAATAAATTTCTATGACCCATTAGTATTCCCCTCTGATGAATTTGATGCATCAATATCTC +AAGTCAACGAGAAGATTAACCAGAGCCTAGCATTTATTCGTAAATCCGATGAATTATTACATAATGTAAA +TGCTGGTAAATCCACCACAAATATCATGATAACTACTATAATTATAGTGATTATAGTAATATTGTTATCA +TTAATTGCTGTTGGACTGCTCTTATACTGTAAGGCCAGAAGCACACCAGTCACACTAAGCAAAGATCAAC +TGAGTGGTATAAATAATATTGCATTTAGTAACTAAATAAAAATAGCACCTAATCATGTTCTTACAATGGT +TTACTATCTGCTCATAGACAACCCATCTGTCATTGGATTTTCTTAAAATCTGAACTTCATCGAAACTCTC +ATCTATAAACCATCTCACTTACACTATTTAAGTAGATTCCTAGTTTATAGTTATATAAAACACAATTGAA +TGCCAGATTAACTTACCATCTGTAAAAATGAAAACTGGGGCAAATATGTCACGAAGGAATCCTTGCAAAT +TTGAAATTCGAGGTCATTGCTTAAATGGTAAGAGGTGTCATTTTAGTCATAATTATTTTGAATGGCCACC +CCATGCACTGCTTGTAAGACAAAACTTTATGTTAAACAGAATACTTAAGTCTATGGATAAAAGTATAGAT +ACCTTATCAGAAATAAGTGGAGCTGCAGAGTTGGACAGAACAGAAGAGTATGCTCTTGGTGTAGTTGGAG +TGCTAGAGAGTTATATAGGATCAATAAACAATATAACTAAACAATCAGCATGTGTTGCCATGAGCAAACT +CCTCACTGAACTCAATAGTGATGATATCAAAAAGCTGAGGGACAATGAAGAGCTAAATTCACCCAAGATA +AGAGTGTACAATACTGTCATATCATATATTGAAAGCAACAGGAAAAACAATAAACAAACTATCCATCTGT +TAAAAAGATTGCCAGCAGACGTATTGAAGAAAACCATCAAAAACACATTGGATATCCATAAGAGCATAAC +CATCAACAACCCAAAAGAATCAACTGTTAGTGATACAAATGACCATGCCAAAAATAATGATACTACCTGA +CAAATATCCTTGTAGTATAACTTCCATACTAATAACAAGTAGATGTAGAGTTACTATGTATAATCAAAAG +AACACACTATATTTCAATCAAAACAACCCAAATAACCATATGTACTCACCGAATCAAACATTCAATGAAA +TCCATTGGACCTCTCAAGAATTGATTGACACAATTCAAATTTTTCTACAACATCTAGGTATTATTGAGGA +TATATATACAATATATATATTAGTGTCATAACACTCAATTCTAACACTCACCACATCGTTACATTATTAA +TTCAAACAATTCAAGTTGTGGGACAAAATGGATCCCATTATTAATGGAAATTCTGCTAATGTTTATCTAA +CCGATAGTTATTTAAAAGGTGTTATCTCTTTCTCAGAGTGTAATGCTTTAGGAAGTTACATATTCAATGG +TCCTTATCTCAAAAATGATTATACCAACTTAATTAGTAGACAAAATCCATTAATAGAACACATGAATCTA +AAGAAACTAAATATAACACAGTCCTTAATATCTAAGTATCATAAAGGTGAAATAAAATTAGAAGAACCTA +CTTATTTTCAGTCATTACTTATGACATACAAGAGTATGACCTCGTCAGAACAGATTGCTACCACTAATTT +ACTTAAAAAGATAATAAGAAGAGCTATAGAAATAAGTGATGTCAAAGTCTATGCTATATTGAATAAACTA +GGGCTTAAAGAAAAGGACAAGATTAAATCCAACAATGGACAAGATGAAGACAACTCAGTTATTACGACCA +TAATCAAAGATGATATACTTTCAGCTGTTAAAGATAATCAATCTCATCTTAAAGCAGACAAAAATCACTC +TACAAAACAAAAAGACACAATCAAAACAACACTCTTGAAGAAATTGATGTGTTCAATGCAACATCCTCCA +TCATGGTTAATACATTGGTTTAACTTATACACAAAATTAAACAACATATTAACACAGTATCGATCAAATG +AGGTAAAAAACCATGGGTTTACATTGATAGATAATCAAACTCTTAGTGGATTTCAATTTATTTTGAACCA +ATATGGTTGTATAGTTTATCATAAGGAACTCAAAAGAATTACTGTGACAACCTATAATCAATTCTTGACA +TGGAAAGATATTAGCCTTAGTAGATTAAATGTTTGTTTAATTACATGGATTAGTAACTGCTTGAACACAT +TAAATAAAAGCTTAGGCTTAAGATGCGGATTCAATAATGTTATCTTGACACAACTATTCCTTTATGGAGA +TTGTATACTAAAGCTATTTCACAATGAGGGGTTCTACATAATAAAAGAGGTAGAGGGATTTATTATGTCT +CTAATTTTAAATATAACAGAAGAAGATCAATTCAGAAAACGATTTTATAATAGTATGCTCAACAACATCA +CAGATGCTGCTAATAAAGCTCAGAAAAATCTGCTATCAAGAGTATGTCATACATTATTAGATAAGACAGT +GTCCGATAATATAATAAATGGCAGATGGATAATTCTATTAAGTAAGTTCCTTAAATTAATTAAGCTTGCA +GGTGACAATAACCTTAACAATCTGAGTGAACTATATTTTTTGTTCAGAATATTTGGACACCCAATGGTAG +ATGAAAGACAAGCCATGGATGCTGTTAAAATTAATTGCAATGAGACCAAATTTTACTTGTTAAGCAGTCT +GAGTATGTTAAGAGGTGCCTTTATATATAGAATTATAAAAGGGTTTGTAAATAATTACAACAGATGGCCT +ACTTTAAGAAATGCTATTGTTTTACCCTTAAGATGGTTAACTTACTATAAACTAAACACTTATCCTTCTT +TGTTGGAACTTACAGAAAGAGATTTGATTGTGTTATCAGGACTACGTTTCTATCGTGAGTTTCGGTTGCC +TAAAAAAGTGGATCTTGAAATGATTATAAATGATAAAGCTATATCACCTCCTAAAAATTTGATATGGACT +AGTTTCCCTAGAAATTACATGCCATCACACATACAAAACTATATAGAACATGAAAAATTAAAATTTTCCG +AGAGTGATAAATCAAGAAGAGTATTAGAGTATTATTTAAGAGATAACAAATTCAATGAATGTGATTTATA +CAACTGTGTAGTTAATCAAAGTTATCTCAACAACCCTAATCATGTGGTATCATTGACAGGCAAAGAAAGA +GAACTCAGTGTAGGTAGAATGTTTGCAATGCAACCGGGAATGTTCAGACAGGTTCAAATATTGGCAGAGA +AAATGATAGCTGAAAACATTTTACAATTCTTTCCTGAAAGTCTTACAAGATATGGTGATCTAGAACTACA +AAAAATATTAGAATTGAAAGCAGGAATAAGTAACAAATCAAATCGCTACAATGATAATTACAACAATTAC +ATTAGTAAGTGCTCTATCATCACAGATCTCAGCAAATTCAATCAAGCATTTCGATATGAAACGTCATGTA +TTTGTAGTGATGTGCTGGATGAACTGCATGGTGTACAATCTCTATTTTCCTGGTTACATTTAACTATTCC +TCATGTCACAATAATATGCACATATAGGCATGCACCCCCCTATATAGGAGATCATATTGTAGATCTTAAC +AATGTAGATGAACAAAGTGGATTATATAGATATCACATGGGTGGCATCGAAGGGTGGTGTCAAAAACTGT +GGACCATAGAAGCTATATCACTATTGGATCTAATATCTCTCAAAGGGAAATTCTCAATTACTGCTTTAAT +TAATGGTGACAATCAATCAATAGATATAAGCAAACCAATCAGACTCATGGAAGGTCAAACTCATGCTCAA +GCAGATTATTTGCTAGCATTAAATAGCCTTAAATTACTGTATAAAGAGTATGCAGGCATAGGCCACAAAT +TAAAAGGAACTGAGACTTATATATCACGAGATATGCAATTTATGAGTAAAACAATTCAACATAACGGTGT +ATATTACCCAGCTAGTATAAAGAAAGTCCTAAGAGTGGGACCGTGGATAAACACTATACTTGATGATTTC +AAAGTGAGTCTAGAATCTATAGGTAGTTTGACACAAGAATTAGAATATAGAGGTGAAAGTCTATTATGCA +GTTTAATATTTAGAAATGTATGGTTATATAATCAGATTGCTCTACAATTAAAAAATCATGCATTATGTAA +CAATAAACTATATTTGGACATATTAAAGGTTCTGAAACACTTAAAAACCTTTTTTAATCTTGATAATATT +GATACAGCATTAACATTGTATATGAATTTACCCATGTTATTTGGTGGTGGTGATCCCAACTTGTTATATC +GAAGTTTCTATAGAAGAACTCCTGACTTCCTCACAGAGGCTATAGTTCACTCTGTGTTCATACTTAGTTA +TTATACAAACCATGACTTAAAAGATAAACTTCAAGATCTGTCAGATGATAGATTGAATAAGTTCTTAACA +TGCATAATCACGTTTGACAAAAACCCTAATGCTGAATTCGTAACATTGATGAGAGATCCTCAAGCTTTAG +GGTCTGAGAGACAAGCTAAAATTACTAGCGAAATCAATAGACTGGCAGTTACAGAGGTTTTGAGTACAGC +TCCAAACAAAATATTCTCCAAAAGTGCACAACATTATACTACTACAGAGATAGATCTAAATGATATTATG +CAAAATATAGAACCTACATATCCTCATGGGCTAAGAGTTGTTTATGAAAGTTTACCCTTTTATAAAGCAG +AGAAAATAGTAAATCTTATATCAGGTACAAAATCTATAACTAACATACTGGAAAAAACTTCTGCCATAGA +CTTAACAGATATTGATAGAGCCACTGAGATGATGAGGAAAAACATAACTTTGCTTATAAGGATACTTCCA +TTGGATTGTAACAGAGATAAAAGAGAGATATTGAGTATGGAAAACCTAAGTATTACTGAATTAAGCAAAT +ATGTTAGGGAAAGATCTTGGTCTTTATCCAATATAGTTGGTGTTACATCACCCAGTATCATGTATACAAT +GGACATCAAATATACTACAAGCACTATATCTAGTGGCATAATTATAGAGAAATATAATGTTAACAGTTTA +ACACGTGGTGAGAGAGGACCCACTAAACCATGGGTTGGTTCATCTACACAAGAGAAAAAAACAATGCCAG +TTTATAATAGACAAGTCTTAACCAAAAAACAGAGAGATCAAATAGATCTATTAGCAAAATTGGATTGGGT +GTATGCATCTATAGATAACAAGGATGAATTCATGGAAGAACTCAGCATAGGAACCCTTGGGTTAACATAT +GAAAAGGCCAAGAAATTATTTCCACAATATTTAAGTGTCAATTATTTGCATCGCCTTACAGTCAGTAGTA +GACCATGTGAATTCCCTGCATCAATACCAGCTTATAGAACAACAAATTATCACTTTGACACTAGCCCTAT +TAATCGCATATTAACAGAAAAGTATGGTGATGAAGATATTGACATAGTATTCCAAAACTGTATAAGCTTT +GGCCTTAGTTTAATGTCAGTAGTAGAACAATTTACTAATGTATGTCCTAACAGAATTATTCTCATACCTA +AGCTTAATGAGATACATTTGATGAAACCTCCCATATTCACAGGTGATGTTGATATTCACAAGTTAAAACA +AGTGATACAAAAACAGCATATGTTTTTACCAGACAAAATAAGTTTGACTCAATATGTGGAATTATTCTTA +AGTAATAAAACACTCAAATCTGGATCTCATGTTAATTCTAATTTAATATTGGCACATAAAATATCTGACT +ATTTTCATAATACTTACATTTTAAGTACTAATTTAGCTGGACATTGGATTCTGATTATACAACTTATGAA +AGATTCTAAAGGTATTTTTGAAAAAGATTGGGGAGAGGGATATATAACTGATCATATGTTTATTAATTTG +AAAGTTTTCTTCAATGCTTATAAGACCTATCTCTTGTGTTTTCATAAAGGTTATGGCAAAGCAAAGCTGG +AGTGTGATATGAACACTTCAGATCTTCTATGTGTATTGGAATTAATAGACAGTAGTTATTGGAAGTCTAT +GTCTAAGGTATTTTTAGAACAAAAAGTTATCAAATACATTCTTAGCCAAGATGCAAGTTTACATAGAGTA +AAAGGATGTCATAGCTTCAAATTATGGTTTCTTAAACGTCTTAATGTAGCAGAATTCACAGTTTGCCCTT +GGGTTGTTAACATAGATTATCATCCAACACATATGAAAGCAATATTAACTTATATAGATCTTGTTAGAAT +GGGATTGATAAATATAGATAGAATACACATTAAAAATAAACACAAATTCAATGATGAATTTTATACTTCT +AATCTCTTCTACATTAATTATAACTTCTCAGATAATACTCATCTATTAACTAAACATATAAGGATTGCTA +ATTCTGAATTAGAAAATAATTACAACAAATTATATCATCCTACACCAGAAACCCTAGAGAATATACTAGC +CAATCCGATTAAAAGTAATGACAAAAAGACACTGAATGACTATTGTATAGGTAAAAATGTTGACTCAATA +ATGTTACCATTGTTATCTAATAAGAAGCTTATTAAATCGTCTGCAATGATTAGAACCAATTACAGCAAAC +AAGATTTGTATAATTTATTCCCTATGGTTGTGATTGATAGAATTATAGATCATTCAGGCAATACAGCCAA +ATCCAACCAACTTTACACTACTACTTCCCACCAAATATCTTTAGTGCACAATAGCACATCACTTTACTGC +ATGCTTCCTTGGCATCATATTAATAGATTCAATTTTGTATTTAGTTCTACAGGTTGTAAAATTAGTATAG +AGTATATTTTAAAAGATCTTAAAATTAAAGATCCCAATTGTATAGCATTCATAGGTGAAGGAGCAGGGAA +TTTATTATTGCGTACAGTAGTGGAACTTCATCCTGACATAAGATATATTTACAGAAGTCTGAAAGATTGC +AATGATCATAGTTTACCTATTGAGTTTTTAAGGCTGTACAATGGACATATCAACATTGATTATGGTGAAA +ATTTGACCATTCCTGCTACAGATGCAACCAACAACATTCATTGGTCTTATTTACATATAAAGTTTGCTGA +ACCTATCAGTCTTTTTGTCTGTGATGCCGAATTGTCTGTAACAGTCAACTGGAGTAAAATTATAATAGAA +TGGAGCAAGCATGTAAGAAAGTGCAAGTACTGTTCCTCAGTTAATAAATGTATGTTAATAGTAAAATATC +ATGCTCAAGATGATATTGATTTCAAATTAGACAATATAACTATATTAAAAACTTATGTATGCTTAGGCAG +TAAGTTAAAGGGATCGGAGGTTTACTTAGTCCTTACAATAGGTCCTGCGAATATATTCCCAGTATTTAAT +GTAGTACAAAATGCTAAATTGATACTATCAAGAACCAAAAATTTCATCATGCCTAAGAAAGCTGATAAAG +AGTCTATTGATGCAAATATTAAAAGTTTGATACCCTTTCTTTGTTACCCTATAACAAAAAAAGGAATTAA +TACTGCATTGTCAAAACTAAAGAGTGTTGTTAGTGGAGATATACTATCATATTCTATAGCTGGACGTAAT +GAAGTTTTCAGCAATAAACTTATAAATCATAAGCATATGAACATCTTAAAATGGTTCAATCATGTTTTAA +ATTTCAGATCAACAGAACTAAACTATAACCATTTATATATGGTAGAATCTACATATCCTTACCTAAGTGA +ATTGTTAAACAGCTTGACAACCAATGAACTTAAAAAACTGATTAAAATCACAGGTAGTCTGTTATACAAC +TTTCATAATGAATAATGAATAAAGATCTTATAATAAAAATTCCCATAGCTATACACTAACACTGTATTCA +ATTATAGTTATTAAAAATTAAAAATCATATAATTTTTTAAATAACTTTTAGTGAACTAATCCTAAAGTTA +TCATTTTAATCTTGGAGGAATAAATTTAAACCCTAATCTAATTGGTTTATATGTGTATTAACTAAATTAC +GAGATATTAGTTTTTGACACTTTTTTTCTCGT +>NC_001781.1 Human orthopneumovirus Subgroup B, complete genome +ACGCGAAAAAATGCGTACTACAAACTTGCACATTCGGAAAAAATGGGGCAAATAAGAATTTGATAAGTGC +TATTTAAGTCTAACCTTTTCAATCAGAAATGGGGTGCAATTCACTGAGCATGATAAAGGTTAGATTACAA +AATTTATTTGACAATGACGAAGTAGCATTGTTAAAAATAACATGTTATACTGACAAATTAATTCTTCTGA +CCAATGCATTAGCCAAAGCAGCAATACATACAATTAAATTAAACGGTATAGTTTTTATACATGTTATAAC +AAGCAGTGAAGTGTGCCCTGATAACAACATTGTAGTAAAATCTAACTTTACAACAATGCCAATATTACAA +AACGGAGGATACATATGGGAATTGATTGAGTTGACACACTGCTCTCAATTAAACGGTCTAATGGATGATA +ATTGTGAAATCAAATTTTCTAAAAGACTAAGTGACTCAGTAATGACTAATTATATGAATCAAATATCTGA +TTTACTTGGGCTTGATCTCAATTCATGAATTATGTTTAGTCTAACTCAATAGACATGTGTTTATTACCAT +TTTAGTTAATATAAAAACTCATCAAAGGGAAATGGGGCAAATAAACTCACCTAATCAATCAAACTATGAG +CACTACAAATGACAACACTACTATGCAAAGATTAATGATCACGGACATGAGACCCCTGTCGATGGATTCA +ATAATAACATCTCTCACCAAAGAAATCATCACACACAAATTCATATACTTGATAAACAATGAATGTATTG +TAAGAAAACTTGATGAAAGACAAGCTACATTTACATTCTTAGTCAATTATGAGATGAAGCTACTGCACAA +AGTAGGGAGTACCAAATACAAGAAATACACTGAATATAATACAAAATATGGCACTTTCCCCATGCCTATA +TTTATCAATCATGGCGGGTTTCTAGAATGTATTGGCATTAAGCCTACAAAACACACTCCTATAATATACA +AATATGACCTCAACCCGTAAATTCCAACAAAAAAAACCAACCCAACCAAACCAAGCTATTCCTCAAACAA +CAATGCTCAATAGTTAAGAAGGAGCTAATCCGTTTTAGTAATTAAAAATAAAAGTAAAGCCAATAACATA +AATTGGGGCAAATACAAAGATGGCTCTTAGCAAAGTCAAGTTAAATGATACATTAAATAAGGATCAGCTG +CTGTCATCCAGCAAATACACTATTCAACGTAGTACAGGAGATAATATTGACACTCCCAATTATGATGTGC +AAAAACACCTAAACAAACTATGTGGTATGCTATTAATCACTGAAGATGCAAATCATAAATTCACAGGATT +AATAGGTATGTTATATGCTATGTCCAGGTTAGGAAGGGAAGACACTATAAAGATACTTAAAGATGCTGGA +TATCATGTTAAAGCTAATGGAGTAGATATAACAACATATCGTCAAGATATAAATGGAAAGGAAATGAAAT +TCGAAGTATTAACATTATCAAGCTTGACATCAGAAATACAAGTCAATATTGAGATAGAATCTAGAAAATC +CTACAAAAAAATGCTAAAAGAGATGGGAGAAGTGGCTCCAGAATATAGGCATGATTCTCCAGACTGTGGG +ATGATAATACTGTGTATAGCAGCACTTGTAATAACCAAATTAGCAGCAGGAGACAGATCAGGTCTTACAG +CAGTAATTAGGAGGGCAAACAATGTCTTAAAAAATGAAATAAAACGCTACAAGGGTCTCATACCAAAGGA +TATAGCTAACAGTTTTTATGAAGTGTTTGAAAAACACCCTCATCTTATAGATGTTTTTGTGCACTTTGGC +ATTGCACAATCATCAACAAGAGGGGGTAGTAGAGTTGAAGGAATCTTTGCAGGATTGTTTATGAATGCCT +ATGGTTCAGGGCAAGTAATGCTAAGATGGGGAGTTTTAGCCAAATCTGTAAAAAATATCATGCTAGGTCA +TGCTAGTGTCCAGGCAGAAATGGAGCAAGTTGTGGAAGTCTATGAGTATGCACAGAAGTTGGGAGGAGAA +GCTGGATTCTACCATATATTGAACAATCCAAAAGCATCATTGCTGTCATTAACTCAATTTCCTAACTTCT +CAAGTGTGGTCCTAGGCAATGCAGCAGGTCTAGGCATAATGGGAGAGTATAGAGGTACGCCAAGAAACCA +GGATCTTTATGATGCAGCCAAAGCATATGCAGAGCAACTCAAAGAAAATGGAGTAATAAACTACAGTGTA +TTAGACTTAACAGCAGAAGAATTGGAAGCCATAAAGAATCAACTCAACCCTAAAGAAGATGATGTAGAGC +TTTAAGTTAACAAAAAATACGGGGCAAATAAGTCAACATGGAGAAGTTTGCACCTGAATTTCATGGAGAA +GATGCAAATAACAAAGCTACCAAATTCCTAGAATCAATAAAGGGCAAGTTCGCATCATCCAAAGATCCTA +AGAAGAAAGATAGCATAATATCTGTTAACTCAATAGATATAGAAGTAACCAAAGAGAGCCCGATAACATC +TGGCACCAACATCATCAATCCAACAAGTGAAGCCGACAGTACCCCAGAAACCAAAGCCAACTACCCAAGA +AAACCCCTAGTAAGCTTCAAAGAAGATCTCACCCCAAGTGACAACCCTTTTTCTAAGTTGTACAAAGAAA +CAATAGAAACATTTGATAACAATGAAGAAGAATCTAGCTACTCATATGAAGAGATAAATGATCAAACAAA +TGACAACATTACAGCAAGACTAGATAGAATTGATGAAAAATTAAGTGAAATATTAGGAATGCTCCATACA +TTAGTAGTTGCAAGTGCAGGACCCACTTCAGCTCGCGATGGAATAAGAGATGCTATGGTTGGTCTGAGAG +AAGAAATGATAGAAAAAATAAGAGCGGAAGCATTAATGACCAATGATAGGTTAGAGGCTATGGCAAGACT +TAGGAATGAGGAAAGCGAAAAAATGGCAAAAGACACCTCAGATGAAGTGCCTCTTAATCCAACTTCCAAA +AAATTGAGTGACTTGTTGGAAGACAACGATAGTGACAATGATCTGTCACTTGATGATTTTTGATCAGTGA +TCAACTCACTCAGCAATCAACAACATCAATAAAACAGACATCAATCCATTGAATCAACTGCCAGACCGAA +CAAACAAATGTCCGTCAGCGGAACCACCAACCAATCAATCAACCAACTGATCCATCAGCAACCTGACGAA +ATTAACAATATAGTAACAAAAAAAGAACAAGATGGGGCAAATATGGAAACATACGTGAACAAGCTTCACG +AAGGCTCCACATACACAGCAGCTGTTCAGTACAATGTTCTAGAAAAAGATGATGATCCTGCATCACTAAC +AATATGGGTGCCTATGTTCCAGTCATCTGTACCAGCAGACTTGCTCATAAAAGAACTTGCAAGCATCAAC +ATACTAGTGAAGCAGATCTCTACGCCCAAAGGACCTTCACTACGAGTCACGATTAACTCAAGAAGTGCTG +TGCTGGCTCAAATGCCTAGTAATTTCATCATAAGCGCAAATGTATCATTAGATGAAAGAAGCAAATTAGC +ATATGATGTAACTACACCTTGTGAAATCAAAGCATGCAGTCTAACATGCTTAAAAGTGAAAAGTATGTTA +ACTACAGTCAAAGATCTTACCATGAAGACATTCAACCCCACTCATGAGATCATTGCTCTATGTGAATTTG +AAAATATTATGACATCAAAAAGAGTAATAATACCAACCTATCTAAGACCAATTAGTGTCAAAAACAAGGA +TCTGAACTCACTAGAAAACATAGCAACCACCGAATTCAAAAATGCTATCACCAATGCGAAAATTATTCCC +TATGCTGGATTAGTATTAGTTATCACAGTTACTGACAATAAAGGAGCATTCAAATATATCAAGCCACAGA +GTCAATTTATAGTAGATCTTGGTGCCTACCTAGAAAAAGAGAGCATATATTATGTGACTACTAATTGGAA +GCATACAGCTACACGTTTTTCAATCAAACCACTAGAGGATTAAATTTAATTATCAACACTGAATGACAGG +TCCACATATATCCTCAAACTACACACTATATCCAAACATCATGAACATCTACACTACACACTTCATCACA +CAAACCAATCCCACTCAAAATCCAAAATCACTACCAGCCACTATCTGCTAGACCTAGAGTGCGAATAGGT +AAATAAAACCAAAATATGGGGTAAATAGACATTAGTTAGAGTTCAATCAATCTCAACAACCATTTATACC +GCCAATTCAATACATATACTATAAATCTTAAAATGGGAAATACATCCATCACAATAGAATTCACAAGCAA +ATTTTGGCCCTATTTTACACTAATACATATGATCTTAACTCTAATCTCTTTACTAATTATAATCACTATT +ATGATTGCAATACTAAATAAGCTAAGTGAACATAAAACATTCTGTAACAATACTCTTGAACTAGGACAGA +TGCATCAAATCAACACATAGTGCTCTACCATCATGCTGTGTCAAATTATAATCCTGTATATATAAACAAA +CAAATCCAATCTTCTCACAGAGTCATGGTGTCGCAAAACCACGCCAACTATCATGGTAGCATAGAGTAGT +TATTTAAAAATTAACATAATGATGAATTATTAGTATGGGATCAAAAACAACATTGGGGCAAATGCAACCA +TGTCCAAACACAAGAATCAACGCACTGCCAGGACTCTAGAAAAGACCTGGGATACTCTCAATCATCTAAT +TGTAATATCCTCTTGTTTATACAGATTAAATTTAAAATCTATAGCACAAATAGCACTATCAGTTCTGGCA +ATGATAATCTCAACCTCTCTCATAATTGCAGCCATAATATTCATCATCTCTGCCAATCACAAAGTTACAC +TAACAACGGTCACAGTTCAAACAATAAAAAACCACACTGAAAAAAACATCACCACCTACCTTACTCAAGT +CCCACCAGAAAGGGTTAGCTCATCCAAACAACCTACAACCACATCACCAATCCACACAAATTCAGCCACA +ACATCACCCAACACAAAGTCAGAAACACACCACACAACAGCACAAACCAAAGGCAGAACCACCACCTCAA +CACAGACCAACAAGCCGAGCACAAAACCACGCCTAAAAAATCCACCAAAAAAACCAAAAGATGATTACCA +TTTTGAAGTGTTCAACTTCGTTCCCTGTAGTATATGTGGCAACAATCAACTTTGCAAATCCATCTGTAAA +ACAATACCAAGCAACAAACCAAAGAAGAAACCAACCATCAAACCCACAAACAAACCAACCACCAAAACCA +CAAACAAAAGAGACCCAAAAACACCAGCCAAAACGACGAAAAAAGAAACTACCACCAACCCAACAAAAAA +ACCAACCCTCACGACCACAGAAAGAGACACCAGCACCTCACAATCCACTGTGCTCGACACAACCACATTA +GAACACACAATCCAACAGCAATCCCTCCACTCAACCACCCCCGAAAACACACCCAACTCCACACAAACAC +CCACAGCATCCGAGCCCTCTACATCAAATTCCACCCAAAATACCCAATCACATGCTTAGTTATTCAAAAA +CTACATCTTAGCAGAAAACCGTGACCTATCAAGCAAGAACGAAATTAAACCTGGGGCAAATAACCATGGA +GCTGCTGATCCACAGGTTAAGTGCAATCTTCCTAACTCTTGCTATTAATGCATTGTACCTCACCTCAAGT +CAGAACATAACTGAGGAGTTTTACCAATCGACATGTAGTGCAGTTAGCAGAGGTTATTTTAGTGCTTTAA +GAACAGGTTGGTATACCAGTGTCATAACAATAGAATTAAGTAATATAAAAGAAACCAAATGCAATGGAAC +TGACACTAAAGTAAAACTTATAAAACAAGAATTAGATAAGTATAAGAATGCAGTGACAGAATTACAGCTA +CTTATGCAAAACACACCAGCTGCCAACAACCGGGCCAGAAGAGAAGCACCACAGTATATGAACTATACAA +TCAATACCACTAAAAACCTAAATGTATCAATAAGCAAGAAGAGGAAACGAAGATTTCTGGGCTTCTTGTT +AGGTGTAGGATCTGCAATAGCAAGTGGTATAGCTGTATCCAAAGTTCTACACCTTGAAGGAGAAGTGAAC +AAGATCAAAAATGCTTTGTTATCTACAAACAAAGCTGTAGTCAGTCTATCAAATGGGGTCAGTGTTTTAA +CCAGCAAAGTGTTAGATCTCAAGAATTACATAAATAACCAATTATTACCCATAGTAAATCAACAGAGCTG +TCGCATCTCCAACATTGAAACAGTTATAGAATTCCAGCAGAAGAACAGCAGATTGTTGGAAATCAACAGA +GAATTCAGTGTCAATGCAGGTGTAACAACACCTTTAAGCACTTACATGTTAACAAACAGTGAGTTACTAT +CATTGATCAATGATATGCCTATAACAAATGATCAGAAAAAATTAATGTCAAGCAATGTTCAGATAGTAAG +GCAACAAAGTTATTCTATCATGTCTATAATAAAGGAAGAAGTCCTTGCATATGTTGTACAGCTACCTATC +TATGGTGTAATAGATACACCTTGCTGGAAATTACACACATCACCTCTATGCACCACCAACATCAAAGAAG +GATCAAATATTTGTTTAACAAGGACTGATAGAGGATGGTATTGTGATAATGCAGGATCAGTATCCTTCTT +TCCACAGGCTGACACTTGTAAAGTACAGTCCAATCGAGTATTTTGTGACACTATGAACAGTTTGACATTA +CCAAGTGAAGTCAGCCTTTGTAACACTGACATATTCAATTCCAAGTATGACTGCAAAATTATGACATCAA +AAACAGACATAAGCAGCTCAGTAATTACTTCTCTTGGAGCTATAGTGTCATGCTATGGTAAAACTAAATG +CACTGCATCCAACAAAAATCGTGGGATTATAAAGACATTTTCTAATGGTTGTGACTATGTGTCAAACAAA +GGAGTAGATACTGTGTCAGTGGGCAACACTTTATACTATGTAAACAAGCTGGAAGGCAAGAACCTTTATG +TAAAAGGGGAACCTATAATAAATTACTATGACCCTCTAGTGTTTCCTTCTGATGAGTTTGATGCATCAAT +ATCTCAAGTCAATGAAAAAATCAATCAAAGTTTAGCTTTTATTCGTAGATCTGATGAATTACTACATAAT +GTAAATACTGGCAAATCTACTACAAATATTATGATAACTACAATTATTATAGTAATCATTGTAGTATTGT +TATCATTAATAGCTATTGGTTTGCTGTTGTATTGCAAAGCCAAAAACACACCAGTTACACTAAGCAAAGA +CCAACTAAGTGGAATCAATAATATTGCATTCAGCAAATAGACAAAAAACCACCTGATCATGTTTCAACAA +CAGTCTGCTGATCACCAATCCCAAATCAACCCATAACAAACACTTCAACATCACAGTACAGGCTGAATCA +TTTCTTCACATCATGCTACCCACACAACTAAGCTAGATCCTTAACTCATAGTTACATAAAAACCTCAAGT +ATCACAATCAAACACTAAATCAACACATCATTCACAAAATTAACAGCTGGGGCAAATATGTCGCGAAGAA +ATCCTTGTAAATTTGAGATTAGAGGTCATTGCTTGAATGGTAGAAGATGTCACTACAGTCATAATTACTT +TGAATGGCCTCCTCATGCCTTACTAGTGAGGCAAAACTTCATGTTAAACAAGATACTCAAGTCAATGGAC +AAAAGCATAGACACTTTGTCTGAAATAAGTGGAGCTGCTGAACTGGACAGAACAGAAGAATATGCTCTTG +GTATAGTTGGAGTGCTAGAGAGTTACATAGGATCTATAAACAACATAACAAAACAATCAGCATGTGTTGC +TATGAGTAAACTTCTTATTGAGATCAATAGTGATGACATTAAAAAGCTGAGAGATAATGAAGAACCCAAT +TCACCTAAGATAAGAGTGTACAATACTGTTATATCATACATTGAGAGCAATAGAAAAAACAACAAGCAAA +CAATCCATCTGCTCAAAAGACTACCAGCAGACGTGCTGAAGAAGACAATAAAAAACACATTAGATATCCA +CAAAAGCATAATCATAAGCAACCCAAAAGAGTCAACCGTGAATGATCAAAATGACCAAACCAAAAATAAT +GATATTACCGGATAAATATCCTTGTAGTATATCATCCATATTGATTTCAAGTGAAAGCATGATTGCTACA +TTCAATCATAAAAACATATTACAATTTAACCATAACCATTTGGATAACCACCAGCGTTTATTAAATAATA +TATTTGATGAAATTCATTGGACACCTAAAAACTTATTAGATGCCACTCAACAATTTCTCCAACATCTTAA +CATCCCTGAAGATATATATACAATATATATATTAGTGTCATAATGCTTGGCCATAACGATTCTATATCAT +CCAACCATAAAACTATCTTAATAAGGTTATGGGACAAAATGGATCCCATTATTAATGGAAACTCTGCTAA +TGTGTATCTAACTGATAGTTATTTAAAAGGTGTTATCTCTTTTTCAGAATGTAATGCTTTAGGGAGTTAC +CTTTTTAACGGCCCTTATCTCAAAAATGATTACACCAACTTAATTAGTAGACAAAGTCCACTACTAGAGC +ATATGAATCTTAAAAAACTAACTATAACACAGTCATTAATATCTAGATATCATAAAGGTGAACTGAAATT +AGAAGAACCAACTTATTTCCAGTCATTACTTATGACATATAAAAGCATGTCCTCGTCTGAACAAATTGCT +ACAACTAACTTACTTAAAAAAATAATACGAAGAGCTATAGAAATAAGTGATGTAAAGGTGTACGCCATCT +TGAATAAACTAGGACTAAAGGAAAAGGACAGAGTTAAGCCCAACAATAATTCAGGTGATGAAAACTCAGT +ACTTACAACTATAATTAAAGATGATATACTTTCGGCTGTGGAAAGCAATCAATCATATACAAATTCAGAC +AAAAATCACTCAGTAAATCAAAATATCACTATCAAAACAACACTCTTGAAAAAATTGATGTGTTCAATGC +AACATCCTCCATCATGGTTAATACACTGGTTCAATTTATATACAAAATTAAATAACATATTAACACAATA +TCGATCAAATGAGGTAAAAAGTCATGGGTTTATATTAATAGATAATCAAACTTTAAGTGGTTTTCAGTTT +ATTTTAAATCAATATGGTTGTATCGTTTATCATAAAGGACTCAAAAAAATCACAACTACTACTTACAATC +AATTTTTAACATGGAAAGACATCAGCCTTAGCAGATTAAATGTTTGCTTAATTACTTGGATAAGTAATTG +TTTGAATACATTAAATAAAAGCTTAGGGCTGAGATGTGGATTCAATAATGTTGTGTTATCACAATTATTT +CTTTATGGAGATTGTATACTGAAATTATTTCATAATGAAGGCTTCTACATAATAAAAGAAGTAGAGGGAT +TTATTATGTCTTTAATTCTAAACATAACAGAAGAAGATCAATTTAGGAAACGATTTTATAATAGCATGCT +AAATAACATCACAGATGCAGCTATTAAGGCTCAAAAGAACCTACTATCAAGGGTATGTCACACTTTATTA +GACAAGACAGTGTCTGATAATATCATAAATGGTAAATGGATAATCCTATTAAGTAAATTTCTTAAATTGA +TTAAGCTTGCAGGTGATAATAATCTCAATAATTTGAGTGAGCTATATTTTCTCTTCAGAATCTTTGGACA +TCCAATGGTTGATGAAAGACAAGCAATGGATGCTGTAAGAATTAACTGTAATGAAACTAAGTTCTACTTA +TTAAGTAGTCTAAGTACGTTAAGAGGTGCTTTCATTTATAGAATCATAAAAGGGTTTGTAAATACCTACA +ACAGATGGCCCACTTTAAGGAATGCTATTGTCCTACCTCTAAGATGGTTAAACTATTATAAACTTAATAC +TTATCCATCTCTACTTGAAATCACAGAAAATGATTTGATTATTTTATCAGGATTGCGGTTCTATCGTGAA +TTTCATCTGCCTAAAAAAGTGGATCTTGAAATGATAATAAATGACAAAGCCATTTCACCTCCAAAAGATC +TAATATGGACTAGTTTTCCTAGAAATTACATGCCATCACATATACAAAATTATATAGAACATGAAAAGTT +GAAGTTCTCTGAAAGCGACAGATCAAGAAGAGTACTAGAGTATTACTTGAGAGATAATAAATTCAATGAA +TGCGATCTATACAATTGTGTAGTCAATCAAAGCTATCTCAACAACTCTAATCACGTGGTATCACTAACTG +GTAAAGAAAGAGAGCTCAGTGTAGGTAGAATGTTTGCTATGCAACCAGGTATGTTTAGGCAAATCCAAAT +CTTAGCAGAGAAAATGATAGCCGAAAATATTTTACAATTCTTCCCTGAGAGTTTGACAAGATATGGTGAT +CTAGAGCTTCAAAAGATATTAGAATTAAAAGCAGGAATAAGCAACAAGTCAAATCGTTATAATGATAACT +ACAACAATTATATCAGTAAATGTTCTATCATTACAGATCTTAGCAAATTCAATCAAGCATTTAGATATGA +AACATCATGTATCTGCAGTGATGTATTAGATGAACTGCATGGAGTACAATCTCTGTTCTCTTGGTTGCAT +TTAACAATACCTCTTGTCACAATAATATGTACATATAGACATGCACCTCCTTTCATAAAGGATCATGTTG +TTAATCTTAATGAAGTTGATGAACAAAGTGGATTATACAGATATCATATGGGTGGTATTGAGGGCTGGTG +TCAAAAACTGTGGACCATTGAAGCTATATCATTATTAGATCTAATATCTCTCAAAGGGAAATTCTCTATC +ACAGCTCTGATAAATGGTGATAATCAGTCAATTGATATAAGTAAACCAGTTAGACTTATAGAGGGTCAGA +CCCATGCTCAAGCAGATTATTTGTTAGCATTAAATAGCCTTAAATTGCTATATAAAGAGTATGCAGGTAT +AGGCCATAAGCTTAAGGGAACAGAGACCTATATATCCCGAGATATGCAGTTCATGAGCAAAACAATCCAG +CACAATGGAGTGTACTATCCAGCCAGTATCAAAAAAGTCCTGAGAGTAGGTCCATGGATAAATACAATAC +TTGATGATTTTAAAGTTAGTTTAGAATCTATAGGTAGCTTAACACAGGAGTTAGAATACAGAGGGGAAAG +CTTATTATGCAGTTTAATATTTAGGAACATTTGGTTATACAATCAAATTGCTTTGCAACTCCGAAATCAT +GCATTATGTAACAATAAGCTATATTTAGATATATTGAAAGTATTAAAACACTTAAAAACTTTTTTTAATC +TTGATAGTATCGATATGGCGTTATCATTGTATATGAATTTGCCTATGCTGTTTGGTGGTGGTGATCCTAA +TTTGTTATATCGAAGCTTTTATAGGAGAACTCCAGACTTCCTTACAGAAGCTATAGTACATTCAGTGTTT +GTGTTGAGCTATTATACTGGTCACGATTTACAAGATAAGCTCCAGGATCTTCCAGATGATAGACTGAACA +AATTCTTGACATGTGTCATCACATTCGATAAAAATCCCAATGCCGAGTTTGTAACATTGATGAGGGATCC +ACAGGCGTTAGGGTCTGAAAGGCAAGCTAAAATTACTAGTGAGATTAATAGATTAGCAGTAACAGAAGTC +TTAAGTATAGCTCCAAACAAAATATTTTCTAAAAGTGCACAACATTATACTACCACTGAGATTGATCTAA +ATGACATTATGCAAAATATAGAACCAACTTACCCTCATGGATTAAGAGTTGTTTATGAAAGTCTACCTTT +TTATAAAGCAGAAAAAATAGTTAATCTTATATCAGGAACAAAATCCATAACTAATATACTTGAAAAAACA +TCAGCAATAGATACAACTGATATTAATAGGGCTACTGATATGATGAGGAAAAATATAACTTTACTTATAA +GGATACTTCCACTAGATTGTAACAAAGACAAAAGAGAGTTATTAAGTTTAGAAAATCTTAGTATAACTGA +ATTAAGCAAGTATGTAAGAGAAAGATCTTGGTCATTATCCAATATAGTAGGAGTAACATCGCCAAGTATT +ATGTTCACAATGGACATTAAATATACAACTAGCACTATAGCCAGTGGTATAATTATAGAAAAATATAATG +TTAATAGTTTAACTCGTGGTGAAAGAGGACCTACTAAGCCATGGGTAGGTTCATCTACGCAGGAGAAAAA +AACAATGCCAGTGTACAATAGACAAGTTTTAACCAAAAAGCAAAGAGACCAAATAGATTTATTAGCAAAA +TTAGACTGGGTATATGCATCCATAGACAACAAAGATGAATTCATGGAAGAACTGAGTACTGGAACACTTG +GACTGTCATATGAAAAAGCCAAAAAGTTGTTTCCACAATATCTAAGTGTCAATTATTTACACCGTTTAAC +AGTCAGTAGTAGACCATGTGAATTCCCTGCATCAATACCAGCTTATAGAACAACAAATTATCATTTCGAT +ACTAGTCCTATCAATCATGTATTAACAGAAAAGTATGGAGATGAAGATATCGACATTGTGTTTCAAAATT +GCATAAGTTTTGGTCTTAGCCTGATGTCGGTTGTGGAACAATTCACAAACATATGTCCTAATAGAATTAT +TCTCATACCGAAGCTGAATGAGATACATTTGATGAAACCTCCTATATTTACAGGAGATGTTGATATCATC +AAGTTGAAGCAAGTGATACAAAAACAGCATATGTTCCTACCAGATAAAATAAGTTTAACCCAATATGTAG +AATTATTCCTAAGTAACAAAGCACTTAAATCTGGATCTAACATCAATTCTAATTTAATATTAGTACATAA +AATGTCTGATTATTTTCATAATGCTTATATTTTAAGTACTAATTTAGCTGGACATTGGATTCTAATTATT +CAACTTATGAAAGATTCAAAAGGTATTTTTGAAAAAGATTGGGGAGAGGGGTACATAACTGATCATATGT +TCATTAATTTGAATGTTTTCTTTAATGCTTATAAGACTTATTTGCTATGTTTTCATAAAGGTTATGGTAA +AGCAAAATTAGAATGTGATATGAACACTTCAGATCTTCTTTGTGTTTTGGAGTTAATAGACAGTAGCTAC +TGGAAATCTATGTCTAAAGTTTTCCTAGAACAAAAAGTCATAAAATACATAGTCAATCAAGACACAAGTT +TGCATAGAATAAAAGGCTGTCACAGTTTTAAGTTGTGGTTTTTAAAACGCCTTAATAATGCTAAATTTAC +CGTATGCCCTTGGGTTGTTAACATAGATTATCACCCAACACATATGAAAGCTATATTATCTTACATAGAT +TTAGTTAGAATGGGGTTAATAAATGTAGATAAATTAACCATTAAAAATAAAAACAAATTCAATGATGAAT +TTTACACATCAAATCTCTTTTACATTAGTTATAACTTTTCAGACAACACTCATTTGCTAACAAAACAAAT +AAGAATTGCTAATTCAGAATTAGAAGATAATTATAACAAACTATATCACCCAACCCCAGAAACTTTAGAA +AATATATCATTAATTCCTGTTAAAAGTAATAATAGTAACAAACCTAAATTTTGTATAAGTGGAAATACCG +AATCTATAATGATGTCAACATTCTCTAATAAAATGCATATTAAATCTTCCACTGTTACCACAAGATTCAA +TTATAGCAAACAAGACTTGTACAATTTATTTCCAAATGTTGTGATAGACAGGATTATAGATCATTCAGGT +AATACAGCAAAATCTAACCAACTTTACATCACCACTTCACATCAGACATCTTTAGTAAGGAATAGTGCAT +CACTTTATTGCATGCTTCCTTGGCATCATGTCAATAGATTTAACTTTGTATTTAGTTCCACAGGATGCAA +GATCAGTATAGAGTATATTTTAAAAGATCTTAAGATTAAGGACCCCAGTTGTATAGCATTCATAGGTGAA +GGAGCTGGTAACTTATTATTACGTACGGTAGTAGAACTTCATCCAGACATAAGATACATTTACAGAAGTT +TAAAAGATTGCAATGATCATAGTTTACCTATTGAATTTCTAAGATTATACAACGGGCATATAAACATAGA +TTATGGTGAGAATTTAACCATTCCTGCTACAGATGCAACTAATAACATTCATTGGTCTTATTTACATATA +AAATTTGCAGAACCTATTAGCATCTTTGTCTGCGATGCTGAATTACCTGTTACAGCCAATTGGAGTAAAA +TTATAATTGAATGGAGTAAGCATGTAAGAAAGTGCAAGTACTGTTCTTCTGTAAATAGATGCATTTTAAT +CGCAAAATATCATGCTCAAGATGATATTGATTTCAAATTAGATAACATTACTATATTAAAAACTTACGTG +TGCCTAGGTAGCAAGTTAAAAGGATCTGAAGTTTACTTAGTCCTTACAATAGGCCCTGCAAATATACTTC +CTGTTTTTGATGTTGTGCAAAATGCTAAATTGATTTTTTCAAGAACTAAAAATTTCATTATGCCTAAAAA +AACTGACAAGGAATCTATCGATGCAAATATTAAAAGCTTAATACCTTTCCTTTGTTACCCTATAACAAAA +AAAGGAATTAAGACTTCATTGTCAAAATTGAAGAGTGTAGTTAATGGGGATATATTATCATATTCTATAG +CTGGACGTAATGAAGTATTCAGCAACAAGCTTATAAACCACAAGCATATGAATATCCTAAAATGGCTAGA +TCATGTTTTAAATTTTAGATCAGCTGAACTTAATTACAATCATTTATACATGATAGAGTCCACATATCCT +TACTTAAGTGAATTGTTAAATAGTTTAACAACCAATGAGCTCAAGAAACTGATTAAAATAACAGGTAGTG +TACTATACAACCTTCCCAACGAACAGTAACTTAAAATATCATTAACAAGTTTGGTCAAATTTAGATGCTA +ACACATCATTATATTATAGTTATTAAAAAATATGCAAACTTTTCAATAATTTAGCTTACTGATTCCAAAA +TTATCATTTTATTTTTAAGGGGTTGAATAAAAGTCTAAAACTAACAATGATACATGTGCATTTACAACAC +AACGAGACATTAGTTTTTGACACTTTTTTTCTCGT + diff --git a/test/data/many-ref-chroms/scheme.bed b/test/data/many-ref-chroms/scheme.bed new file mode 100644 index 0000000..cd6790a --- /dev/null +++ b/test/data/many-ref-chroms/scheme.bed @@ -0,0 +1,8 @@ +NC_038235.1 type_a 0 21 scheme-a_1_LEFT_0 1 + +NC_038235.1 type_a 1213 1233 scheme-a_1_RIGHT_0 1 - +NC_038235.1 type_a 1123 1144 scheme-a_2_LEFT_0 2 + +NC_038235.1 type_a 2123 2143 scheme-a_2_RIGHT_0 2 - +NC_001781.1 type_b 0 21 scheme-b_1_LEFT_0 1 + +NC_001781.1 type_b 1213 1233 scheme-b_1_RIGHT_0 1 - +NC_001781.1 type_b 1123 1144 scheme-b_2_LEFT_0 2 + +NC_001781.1 type_b 2123 2143 scheme-b_2_RIGHT_0 2 - diff --git a/test/data/primer-schemes/artic/v4.1/info.yml b/test/data/primer-schemes/artic/v4.1/info.yml deleted file mode 100644 index e11bcdb..0000000 --- a/test/data/primer-schemes/artic/v4.1/info.yml +++ /dev/null @@ -1,20 +0,0 @@ -schema_version: 0.9.0 -name: artic-v4.1 -organism: sars-cov-2 -aliases: -- ARTIC/V4.1 -developers: -- organisation_name: ARTIC network - home_page: https://artic.network/ -vendors: -- organisation_name: IDT - kit_name: '10011442' -- organisation_name: Eurofins - home_page: https://eurofinsgenomics.com -amplicon_size: 400 -repository_url: https://github.com/pha4ge/primer-schemes/tree/main/sars-cov-2/artic/v4.1 -citations: -- https://doi.org/10.1101%2F2020.09.04.283077 -derived_from: artic-v4 -primer_checksum: primaschema:9005b441227985c8 -reference_checksum: primaschema:7d5621cd3b3e498d diff --git a/test/data/primer-schemes/artic/v4.1/primer.bed b/test/data/primer-schemes/artic/v4.1/primer.bed deleted file mode 100644 index 5b8e1d4..0000000 --- a/test/data/primer-schemes/artic/v4.1/primer.bed +++ /dev/null @@ -1,209 +0,0 @@ -MN908947.3 25 50 SARS-CoV-2_1_LEFT 1 + AACAAACCAACCAACTTTCGATCTC -MN908947.3 324 344 SARS-CoV-2_2_LEFT 2 + TTTACAGGTTCGCGACGTGC -MN908947.3 408 431 SARS-CoV-2_1_RIGHT 1 - CTTCTACTAAGCCACAAGTGCCA -MN908947.3 644 666 SARS-CoV-2_3_LEFT 1 + GTAATAAAGGAGCTGGTGGCCA -MN908947.3 705 727 SARS-CoV-2_2_RIGHT 2 - ATAAGGATCAGTGCCAAGCTCG -MN908947.3 944 966 SARS-CoV-2_4_LEFT 2 + GTGTATACTGCTGCCGTGAACA -MN908947.3 1017 1044 SARS-CoV-2_3_RIGHT 1 - GCCAATTTAATTTCAAAAGGTGTCTGC -MN908947.3 1245 1266 SARS-CoV-2_5_LEFT 1 + TGAAACTTCATGGCAGACGGG -MN908947.3 1337 1362 SARS-CoV-2_4_RIGHT 2 - ACAACAGCATTTTGGGGTAAGTAAC -MN908947.3 1540 1562 SARS-CoV-2_6_LEFT 2 + CGTGCTAGCGCTAACATAGGTT -MN908947.3 1623 1650 SARS-CoV-2_5_RIGHT 1 - TTGATGTTGACTTTCTCTTTTTGGAGT -MN908947.3 1851 1875 SARS-CoV-2_7_LEFT 1 + ACTGAGTCCTCTTTATGCATTTGC -MN908947.3 1925 1948 SARS-CoV-2_6_RIGHT 2 - AACACGCACAGAATTTTGAGCAG -MN908947.3 2154 2180 SARS-CoV-2_8_LEFT 2 + GCTTGAAGAGAAGTTTAAGGAAGGTG -MN908947.3 2228 2250 SARS-CoV-2_7_RIGHT 1 - CCACCGACAATTTCACAAGCAC -MN908947.3 2483 2508 SARS-CoV-2_9_LEFT 1 + TCTTCTTAGAGGGAGAAACACTTCC -MN908947.3 2544 2571 SARS-CoV-2_8_RIGHT 2 - GGTTGTTCTAATGGTTGTAAATCACCA -MN908947.3 2780 2813 SARS-CoV-2_10_LEFT_alt1 2 + TGAATATCACTTTTGAACTTGATGAAAGGATTG -MN908947.3 2826 2850 SARS-CoV-2_10_LEFT 2 + TGAGAAGTGCTCTGCCTATACAGT -MN908947.3 2861 2885 SARS-CoV-2_9_RIGHT 1 - CACAGGCGAACTCATTTACTTCTG -MN908947.3 3078 3102 SARS-CoV-2_11_LEFT 1 + AGAAGAGTTTGAGCCATCAACTCA -MN908947.3 3156 3177 SARS-CoV-2_10_RIGHT_alt1 2 - GGTTGAAGAGCAGCAGAAGTG -MN908947.3 3183 3210 SARS-CoV-2_10_RIGHT 2 - TCATCTAACCAATCTTCTTCTTGCTCT -MN908947.3 3390 3412 SARS-CoV-2_12_LEFT 2 + TGCAGACATTGTGGAAGAAGCT -MN908947.3 3470 3492 SARS-CoV-2_11_RIGHT 1 - TTTAAGGCTCCTGCAACACCTC -MN908947.3 3683 3705 SARS-CoV-2_13_LEFT 1 + AGCACGAAGTTCTACTTGCACC -MN908947.3 3769 3794 SARS-CoV-2_12_RIGHT 2 - CAGCTAAGTAGACATTTGTGCGAAC -MN908947.3 3992 4018 SARS-CoV-2_14_LEFT 2 + TGGAAGAAACTAAGTTCCTCACAGAA -MN908947.3 4067 4093 SARS-CoV-2_13_RIGHT 1 - GATGTCAATGTCACTAACAAGAGTGG -MN908947.3 4312 4339 SARS-CoV-2_15_LEFT 1 + AAAAGTGCCTTTTACATTCTACCATCT -MN908947.3 4387 4409 SARS-CoV-2_14_RIGHT 2 - CATGTGCAAGCATTTCTCGCAA -MN908947.3 4620 4648 SARS-CoV-2_16_LEFT 2 + TGTAACACATGGCTTAAATTTGGAAGAA -MN908947.3 4685 4710 SARS-CoV-2_15_RIGHT 1 - GCATCAGGTGAAGAAACAGAAACTG -MN908947.3 4923 4953 SARS-CoV-2_17_LEFT 1 + TGACAATCTTAAGACACTTCTTTCTTTGAG -MN908947.3 4995 5017 SARS-CoV-2_16_RIGHT 2 - CACAACTTGCGTGTGGAGGTTA -MN908947.3 5230 5259 SARS-CoV-2_18_LEFT 2 + TGGAAATACCCACAAGTTAATGGTTTAAC -MN908947.3 5302 5331 SARS-CoV-2_17_RIGHT 1 - TTCAACTCTATTTGTTGGAGTGTTAACAA -MN908947.3 5561 5584 SARS-CoV-2_19_LEFT 1 + AAGCTGTTATGTACATGGGCACA -MN908947.3 5620 5643 SARS-CoV-2_18_RIGHT 2 - GCTTGTTTACCACACGTACAAGG -MN908947.3 5867 5894 SARS-CoV-2_20_LEFT 2 + ACAAAGAAAACAGTTACACAACAACCA -MN908947.3 5932 5957 SARS-CoV-2_19_RIGHT 1 - TGTCCAACTTAGGGTCAATTTCTGT -MN908947.3 6184 6210 SARS-CoV-2_21_LEFT 1 + CACTACACACCCTCTTTTAAGAAAGG -MN908947.3 6247 6272 SARS-CoV-2_20_RIGHT 2 - ACGTGGCTTTATTAGTTGCATTGTT -MN908947.3 6478 6507 SARS-CoV-2_22_LEFT 2 + GTAGGAGACATTATACTTAAACCAGCAAA -MN908947.3 6553 6582 SARS-CoV-2_21_RIGHT 1 - GTAAGACTAGAATTGTCTACATAAGCAGC -MN908947.3 6747 6776 SARS-CoV-2_23_LEFT 1 + AAACCGTGTTTGTACTAATTATATGCCTT -MN908947.3 6859 6885 SARS-CoV-2_22_RIGHT 2 - CCGACACTCTTAACAGTATTCTTTGC -MN908947.3 7057 7084 SARS-CoV-2_24_LEFT 2 + GGTTACAGAGAAGGCTATTTGAACTCT -MN908947.3 7122 7148 SARS-CoV-2_23_RIGHT 1 - AACCACTAAGACAAACACTACAAGGT -MN908947.3 7127 7156 SARS-CoV-2_23_RIGHT_alt1 1 - AGAATCTAAACCACTAAGACAAACACTAC -MN908947.3 7381 7403 SARS-CoV-2_25_LEFT 1 + CAAATGGCCCCGATTTCAGCTA -MN908947.3 7440 7467 SARS-CoV-2_24_RIGHT 2 - ACAACATGCACATAACTTTTCCATACA -MN908947.3 7672 7695 SARS-CoV-2_26_LEFT 2 + GCGAGAGACTTGTCACTACAGTT -MN908947.3 7747 7770 SARS-CoV-2_25_RIGHT 1 - TGGATGGAACCATTCTTCACTGT -MN908947.3 7997 8019 SARS-CoV-2_27_LEFT 1 + CTGATGTTGGTGATAGTGCGGA -MN908947.3 8063 8092 SARS-CoV-2_26_RIGHT 2 - GAGTTTTTCCATTGGTACGTTAAAAGTTG -MN908947.3 8304 8326 SARS-CoV-2_28_LEFT 2 + TGAAAACATGACACCCCGTGAC -MN908947.3 8367 8392 SARS-CoV-2_27_RIGHT_alt1 1 - AATGTTGTGACTTTTTGCTACCTGC -MN908947.3 8370 8395 SARS-CoV-2_27_RIGHT 1 - AGCAATGTTGTGACTTTTTGCTACC -MN908947.3 8596 8619 SARS-CoV-2_29_LEFT 1 + CTTGTGTTCCTTTTTGTTGCTGC -MN908947.3 8691 8714 SARS-CoV-2_28_RIGHT 2 - TGACACCACCATCAATAGCCTTG -MN908947.3 8919 8944 SARS-CoV-2_30_LEFT 2 + ACCTAGAGTTTTTAGTGCAGTTGGT -MN908947.3 8990 9013 SARS-CoV-2_29_RIGHT 1 - AGCCAAAACACAAGCTGATGTTG -MN908947.3 9168 9192 SARS-CoV-2_31_LEFT 1 + CCTTGAAGGTTCTGTTAGAGTGGT -MN908947.3 9306 9329 SARS-CoV-2_30_RIGHT 2 - CTACACCACAGAAAACTCCTGGT -MN908947.3 9470 9497 SARS-CoV-2_32_LEFT 2 + GAGCTTTTGGTGAATACAGTCATGTAG -MN908947.3 9535 9564 SARS-CoV-2_31_RIGHT 1 - AATGAGTAAACTGGTGTTAAACAGAGTAC -MN908947.3 9782 9805 SARS-CoV-2_33_LEFT 1 + GTACTTTTGAAGAAGCTGCGCTG -MN908947.3 9842 9866 SARS-CoV-2_32_RIGHT 2 - GAGGTAATAGCACATCACTACGCA -MN908947.3 10076 10099 SARS-CoV-2_34_LEFT 2 + TCCCATCTGGTAAAGTTGAGGGT -MN908947.3 10150 10176 SARS-CoV-2_33_RIGHT 1 - TGTCTTGGACAGTAAACTACGTCATC -MN908947.3 10393 10419 SARS-CoV-2_35_LEFT 1 + GTGTTAGCTTGTTACAATGGTTCACC -MN908947.3 10465 10491 SARS-CoV-2_34_RIGHT 2 - CCACATGAACCATTAAGGAATGAACC -MN908947.3 10713 10742 SARS-CoV-2_36_LEFT 2 + CAATCGATTTACCACAACTCTTAATGACT -MN908947.3 10785 10810 SARS-CoV-2_35_RIGHT 1 - AGGTCCTAGTATGTCAACATGGTCT -MN908947.3 11000 11023 SARS-CoV-2_37_LEFT 1 + CACACCACTGGTTGTTACTCACA -MN908947.3 11092 11116 SARS-CoV-2_36_RIGHT 2 - ACCCATAGCAAAAGGTAAAAAGGC -MN908947.3 11305 11330 SARS-CoV-2_38_LEFT 2 + GACTGTGTTATGTATGCATCAGCTG -MN908947.3 11388 11414 SARS-CoV-2_37_RIGHT 1 - GTGTCAAGACATTCATAAGTGTCCAC -MN908947.3 11624 11651 SARS-CoV-2_39_LEFT 1 + GCTATTTTTGTACTTGTTACTTTGGCC -MN908947.3 11689 11720 SARS-CoV-2_38_RIGHT 2 - CCTGTGTAGAAACTAAGTAATCATAAACACC -MN908947.3 11937 11963 SARS-CoV-2_40_LEFT 2 + TGTCCAGTTACACAATGACATTCTCT -MN908947.3 12011 12033 SARS-CoV-2_39_RIGHT 1 - CCCTGCATGGAAAGCAAAACAG -MN908947.3 12234 12255 SARS-CoV-2_41_LEFT 1 + ATTTGACCGTGATGCAGCCAT -MN908947.3 12317 12339 SARS-CoV-2_40_RIGHT 2 - ACTTTTGCCCTCTTGTCCTCAG -MN908947.3 12519 12546 SARS-CoV-2_42_LEFT 2 + TGGTACAACATTTACTTATGCATCAGC -MN908947.3 12618 12643 SARS-CoV-2_41_RIGHT 1 - AAGAGGCCATGCTAAATTAGGTGAA -MN908947.3 12831 12856 SARS-CoV-2_43_LEFT 1 + GGATTTGAAATGGGCTAGATTCCCT -MN908947.3 12895 12920 SARS-CoV-2_42_RIGHT 2 - TGTCTGTAACAAACCTACAAGGTGG -MN908947.3 13124 13148 SARS-CoV-2_44_LEFT 2 + GGGGACAACCAATCACTAATTGTG -MN908947.3 13218 13240 SARS-CoV-2_43_RIGHT 1 - CGATGCACCACCAAAGGATTCT -MN908947.3 13463 13485 SARS-CoV-2_45_LEFT 1 + TAAACGGGTTTGCGGTGTAAGT -MN908947.3 13506 13528 SARS-CoV-2_44_RIGHT 2 - CATCAGTACTAGTGCCTGTGCC -MN908947.3 13752 13775 SARS-CoV-2_46_LEFT 2 + AGAATAGACGGTGACATGGTACC -MN908947.3 13833 13859 SARS-CoV-2_45_RIGHT 1 - TCACAATTACCTTCATCAAAATGCCT -MN908947.3 14045 14075 SARS-CoV-2_47_LEFT 1 + TGGTGTACTGACATTAGATAATCAAGATCT -MN908947.3 14120 14144 SARS-CoV-2_46_RIGHT 2 - TCTACAACAGGAACTCCACTACCT -MN908947.3 14338 14362 SARS-CoV-2_48_LEFT 2 + ACTGTTTGGATGACAGATGCATTC -MN908947.3 14428 14457 SARS-CoV-2_47_RIGHT 1 - TGGAACACCATCAACAAATATTTTTCTCA -MN908947.3 14647 14674 SARS-CoV-2_49_LEFT 1 + ACAATGTTGCTTTTCAAACTGTCAAAC -MN908947.3 14717 14743 SARS-CoV-2_48_RIGHT 2 - CAGAACTTCCTTCCTTAAAGAAACCC -MN908947.3 14953 14983 SARS-CoV-2_50_LEFT 2 + CATTTAATAAATGGGGTAAGGCTAGACTTT -MN908947.3 15023 15050 SARS-CoV-2_49_RIGHT 1 - GGGATGACATTACGTTTTGTATATGCG -MN908947.3 15214 15237 SARS-CoV-2_51_LEFT 1 + GCAAATTCTATGGTGGTTGGCAC -MN908947.3 15336 15358 SARS-CoV-2_50_RIGHT 2 - GAGCAAGAACAAGTGAGGCCAT -MN908947.3 15535 15557 SARS-CoV-2_52_LEFT 2 + CTGTCACGGCCAATGTTAATGC -MN908947.3 15596 15619 SARS-CoV-2_51_RIGHT 1 - GTCTGTGTTGTAAATTGCGGACA -MN908947.3 15855 15881 SARS-CoV-2_53_LEFT 1 + ACTAAAGGACCTCATGAATTTTGCTC -MN908947.3 15917 15941 SARS-CoV-2_52_RIGHT 2 - GGATCTGGGTAAGGAAGGTACACA -MN908947.3 16112 16137 SARS-CoV-2_54_LEFT 2 + ACATGATGAGTTAACAGGACACATG -MN908947.3 16239 16260 SARS-CoV-2_53_RIGHT 1 - GCAAAGAACACAAGCCCCAAC -MN908947.3 16386 16408 SARS-CoV-2_55_LEFT 1 + AATGCTCCAGGTTGTGATGTCA -MN908947.3 16483 16508 SARS-CoV-2_54_RIGHT 2 - CCAAAAACTTGTCCATTAGCACACA -MN908947.3 16692 16714 SARS-CoV-2_56_LEFT 2 + ACTGTACGTGAAGTGCTGTCTG -MN908947.3 16767 16796 SARS-CoV-2_55_RIGHT 1 - ACACGATAACCAGTAAAGACATAATTTCG -MN908947.3 16986 17013 SARS-CoV-2_57_LEFT 1 + GGCTTATACCCAACACTCAATATCTCA -MN908947.3 17082 17105 SARS-CoV-2_56_RIGHT 2 - TGACTCTTACCAGTACCAGGTGG -MN908947.3 17323 17345 SARS-CoV-2_58_LEFT 2 + TGCCTGAGACGACAGCAGATAT -MN908947.3 17381 17405 SARS-CoV-2_57_RIGHT 1 - CTGGCATTGACAACACTCAAATCA -MN908947.3 17615 17642 SARS-CoV-2_59_LEFT 1 + GCTTAAAGCACATAAAGACAAATCAGC -MN908947.3 17688 17711 SARS-CoV-2_58_RIGHT 2 - TGTGGCCTGTTAATTGCAGATGA -MN908947.3 17911 17939 SARS-CoV-2_60_LEFT 2 + ACAGATTTAATGTTGCTATTACCAGAGC -MN908947.3 17997 18022 SARS-CoV-2_59_RIGHT 1 - TCCTACGTGGAATTTCAAGACTTGT -MN908947.3 18244 18267 SARS-CoV-2_61_LEFT 1 + ACCCTAACATGTTTATCACCCGC -MN908947.3 18307 18328 SARS-CoV-2_60_RIGHT 2 - TAGCATGACACCCCTCGACAT -MN908947.3 18550 18578 SARS-CoV-2_62_LEFT 2 + GTGACACACTTAAAAATCTCTCTGACAG -MN908947.3 18624 18652 SARS-CoV-2_61_RIGHT 1 - GCTCAGGTCCTATTTTCACAAAATACTT -MN908947.3 18869 18891 SARS-CoV-2_63_LEFT 1 + TAGGTGTCTAGCTGTCCACGAG -MN908947.3 18936 18961 SARS-CoV-2_62_RIGHT 2 - CCGCATTAATCTTCAGTTCATCACC -MN908947.3 19183 19208 SARS-CoV-2_64_LEFT 2 + GCCTATTTTGGAATTGCAATGTCGA -MN908947.3 19252 19277 SARS-CoV-2_63_RIGHT 1 - CCAGGCAAGTTAAGGTTAGATAGCA -MN908947.3 19485 19513 SARS-CoV-2_65_LEFT 1 + GTCTGTAGACATCATGCTAATGAGTACA -MN908947.3 19558 19586 SARS-CoV-2_64_RIGHT 2 - GTATCAAATTGTTTGTAAACCCACAAGC -MN908947.3 19810 19836 SARS-CoV-2_66_LEFT 2 + AACCAGTACCAGAGGTGAAAATACTC -MN908947.3 19877 19901 SARS-CoV-2_65_RIGHT 1 - GCTGGAGCATCTCTTTTGTAGTCC -MN908947.3 20090 20117 SARS-CoV-2_67_LEFT 1 + CAAACAAGCTAGTCTTAATGGAGTCAC -MN908947.3 20186 20216 SARS-CoV-2_66_RIGHT 2 - TTTCTACTCTGAGTAAAGTAAGTTTCAGGT -MN908947.3 20377 20405 SARS-CoV-2_68_LEFT 2 + GACTAGCTAAACGTTTTAAGGAATCACC -MN908947.3 20472 20497 SARS-CoV-2_67_RIGHT 1 - AACACACACACTTAGATGAACCTGT -MN908947.3 20677 20699 SARS-CoV-2_69_LEFT 1 + CGGGTGTTGCTATGCCTAATCT -MN908947.3 20766 20792 SARS-CoV-2_68_RIGHT 2 - GCGACATTCATCATTATGCCTTTAGG -MN908947.3 20988 21013 SARS-CoV-2_70_LEFT 2 + TTGATTGGTGATTGTGCAACTGTAC -MN908947.3 21050 21080 SARS-CoV-2_69_RIGHT 1 - TTTGTAACATTTTTAGTCTTAGGGTCGTAC -MN908947.3 21294 21316 SARS-CoV-2_71_LEFT 1 + GGCAAACCACGCGAACAAATAG -MN908947.3 21358 21387 SARS-CoV-2_70_RIGHT 2 - AGAATAGGAAGACAACTGAATTGGATTTG -MN908947.3 21532 21561 SARS-CoV-2_72_LEFT 2 + GTGATGTTCTTGTTAACAACTAAACGAAC -MN908947.3 21675 21700 SARS-CoV-2_71_RIGHT 1 - TGAGGATCTGAAAACTTTGTCAGGG -MN908947.3 21865 21889 SARS-CoV-2_73_LEFT 1 + AGAGGCTGGATTTTTGGTACTACT -MN908947.3 21904 21933 SARS-CoV-2_72_RIGHT 2 - GTAGCGTTATTAACAATAAGTAGGGACTG -MN908947.3 22091 22113 SARS-CoV-2_74_LEFT 2 + TGGACCTTGAAGGAAAACAGGG -MN908947.3 22247 22274 SARS-CoV-2_73_RIGHT 1 - ACCTAGTGATGTTAATACCTATTGGCA -MN908947.3 22402 22428 SARS-CoV-2_75_LEFT 1 + GAAAATGGAACCATTACAGATGCTGT -MN908947.3 22474 22503 SARS-CoV-2_74_RIGHT 2 - TGATAGATTCCTTTTTCTACAGTGAAGGA -MN908947.3 22648 22677 SARS-CoV-2_76_LEFT 2 + GCTGATTATTCTGTCCTATATAATTCCGC -MN908947.3 22742 22774 SARS-CoV-2_76_LEFT_alt1 2 + ATGTCTATGCAGATTCATTTGTAATTAGAGGT -MN908947.3 22785 22805 SARS-CoV-2_75_RIGHT 1 - TTTGCCCTGGAGCGATTTGT -MN908947.3 22944 22974 SARS-CoV-2_77_LEFT 1 + CAAACCTTTTGAGAGAGATATTTCAACTGA -MN908947.3 23028 23057 SARS-CoV-2_76_RIGHT 2 - GTTGGAAACCATATGATTGTAAAGGAAAG -MN908947.3 23120 23141 SARS-CoV-2_76_RIGHT_alt1 2 - GTCCACAAACAGTTGCTGGTG -MN908947.3 23219 23246 SARS-CoV-2_78_LEFT 2 + CTGAGTCTAACAAAAAGTTTCTGCCTT -MN908947.3 23327 23351 SARS-CoV-2_77_RIGHT 1 - CACTGACACCACCAAAAGAACATG -MN908947.3 23553 23575 SARS-CoV-2_79_LEFT 1 + ACCCATTGGTGCAGGTATATGC -MN908947.3 23611 23635 SARS-CoV-2_78_RIGHT 2 - GGATTGACTAGCTACACTACGTGC -MN908947.3 23853 23876 SARS-CoV-2_80_LEFT 2 + CCGTGCTTTAACTGGAATAGCTG -MN908947.3 23914 23944 SARS-CoV-2_79_RIGHT_alt1 1 - AATTGGTGGTGTTTTGTAAATTTGTTTGAC -MN908947.3 23927 23955 SARS-CoV-2_79_RIGHT 1 - CCAAAATCTTTAATTGGTGGTGTTTTGT -MN908947.3 24171 24194 SARS-CoV-2_81_LEFT 1 + TGCTCAATACACTTCTGCACTGT -MN908947.3 24233 24258 SARS-CoV-2_80_RIGHT 2 - GCAAATGGTATTTGTAATGCAGCAC -MN908947.3 24426 24448 SARS-CoV-2_82_LEFT 2 + TGCACAAGCTTTAAACACGCTT -MN908947.3 24545 24567 SARS-CoV-2_81_RIGHT 1 - TGAAGTCTGCCTGTGATCAACC -MN908947.3 24750 24772 SARS-CoV-2_83_LEFT 1 + GCATGTGACTTATGTCCCTGCA -MN908947.3 24814 24836 SARS-CoV-2_82_RIGHT 2 - CACGAGGAAAGTGTGCTTTTCC -MN908947.3 25051 25076 SARS-CoV-2_84_LEFT 2 + GTTGATTTAGGTGACATCTCTGGCA -MN908947.3 25122 25150 SARS-CoV-2_83_RIGHT 1 - AGATTCATTTAAATTCTTGGCAACCTCA -MN908947.3 25331 25353 SARS-CoV-2_85_LEFT 1 + ATGAAGACGACTCTGAGCCAGT -MN908947.3 25438 25461 SARS-CoV-2_84_RIGHT 2 - AGCATCCTTGATTTCACCTTGCT -MN908947.3 25645 25672 SARS-CoV-2_86_LEFT 2 + TGTTGTTTGTAACAGTTTACTCACACC -MN908947.3 25711 25740 SARS-CoV-2_85_RIGHT 1 - CTGCAAGAAGTAGACTAAAGCATAAAGAT -MN908947.3 25951 25979 SARS-CoV-2_87_LEFT 1 + GTGGTTATACTGAAAAATGGGAATCTGG -MN908947.3 26026 26050 SARS-CoV-2_86_RIGHT 2 - TCAATTGAGTTGAGTACAGCTGGT -MN908947.3 26242 26268 SARS-CoV-2_88_LEFT_alt1 2 + TTATGTACTCATTCGTTTCGGAAGAG -MN908947.3 26255 26277 SARS-CoV-2_88_LEFT 2 + CGTTTCGGAAGAGACAGGTACG -MN908947.3 26338 26360 SARS-CoV-2_87_RIGHT 1 - AATCGAAGCGCAGTAAGGATGG -MN908947.3 26564 26587 SARS-CoV-2_89_LEFT 1 + AAGCTCCTTGAACAATGGAACCT -MN908947.3 26592 26621 SARS-CoV-2_89_LEFT_alt1 1 + TAGGTTTCCTATTCCTTACATGGATTTGT -MN908947.3 26635 26661 SARS-CoV-2_88_RIGHT 2 - ACAAAAACCTATTCCTGTTGGCATAG -MN908947.3 26873 26895 SARS-CoV-2_90_LEFT 2 + ATTCTTCTCAACGTGCCACTCC -MN908947.3 26956 26979 SARS-CoV-2_89_RIGHT 1 - CAGCAATACGAAGATGTCCACGA -MN908947.3 26966 26991 SARS-CoV-2_89_RIGHT_alt1 1 - CTAGATGGTGTCCAGCAATACGAAG -MN908947.3 27152 27177 SARS-CoV-2_91_LEFT 1 + TCCAGTAGCAGTGACAATATTGCTT -MN908947.3 27218 27251 SARS-CoV-2_90_RIGHT_alt1 2 - ATTAGTAATATCTCTGCTATAGTAACCTGAAAG -MN908947.3 27256 27283 SARS-CoV-2_90_RIGHT 2 - TCCAAATGGAAACTTTAAAAGTCCTCA -MN908947.3 27447 27473 SARS-CoV-2_92_LEFT 2 + CACTACCAAGAGTGTGTTAGAGGTAC -MN908947.3 27534 27560 SARS-CoV-2_91_RIGHT 1 - AGTGCAAATTTGTTATCAGCTAGAGG -MN908947.3 27700 27726 SARS-CoV-2_93_LEFT 1 + TTGTTGCGGCAATAGTGTTTATAACA -MN908947.3 27826 27855 SARS-CoV-2_92_RIGHT 2 - GTTCAAGTGAGAACCAAAAGATAATAAGC -MN908947.3 27996 28021 SARS-CoV-2_94_LEFT 2 + ACCCGTGTCCTATTCACTTCTATTC -MN908947.3 28082 28104 SARS-CoV-2_93_RIGHT 1 - TGGGTGATTTAGAACCAGCCTC -MN908947.3 28190 28214 SARS-CoV-2_95_LEFT 1 + GTGCGTTGTTCGTTCTATGAAGAC -MN908947.3 28394 28416 SARS-CoV-2_94_RIGHT 2 - TTATTGGGTAAACCTTGGGGCC -MN908947.3 28512 28536 SARS-CoV-2_96_LEFT 2 + AGATGACCAAATTGGCTACTACCG -MN908947.3 28572 28598 SARS-CoV-2_95_RIGHT 1 - ACCATCTTGGACTGAGATCTTTCATT -MN908947.3 28827 28849 SARS-CoV-2_97_LEFT 1 + TTCCTCATCACGTAGTCGCAAC -MN908947.3 28893 28914 SARS-CoV-2_96_RIGHT 2 - CCATTGCCAGCCATTCTAGCA -MN908947.3 29136 29161 SARS-CoV-2_98_LEFT 2 + CCAGGAACTAATCAGACAAGGAACT -MN908947.3 29206 29227 SARS-CoV-2_97_RIGHT 1 - CGACATTCCGAAGAACGCTGA -MN908947.3 29452 29475 SARS-CoV-2_99_LEFT 1 + CTTCTTCCTGCTGCAGATTTGGA -MN908947.3 29512 29534 SARS-CoV-2_98_RIGHT 2 - TTTAGGCCTGAGTTGAGTCAGC -MN908947.3 29827 29854 SARS-CoV-2_99_RIGHT 1 - GCTATTAAAATCACATGGGGATAGCAC diff --git a/test/data/primer-schemes/artic/v4.1/scheme.bed b/test/data/primer-schemes/artic/v4.1/scheme.bed deleted file mode 100644 index 0f9e5b9..0000000 --- a/test/data/primer-schemes/artic/v4.1/scheme.bed +++ /dev/null @@ -1,209 +0,0 @@ -MN908947.3 25 50 SARS-CoV-2_1_LEFT 1 + -MN908947.3 324 344 SARS-CoV-2_2_LEFT 2 + -MN908947.3 408 431 SARS-CoV-2_1_RIGHT 1 - -MN908947.3 644 666 SARS-CoV-2_3_LEFT 1 + -MN908947.3 705 727 SARS-CoV-2_2_RIGHT 2 - -MN908947.3 944 966 SARS-CoV-2_4_LEFT 2 + -MN908947.3 1017 1044 SARS-CoV-2_3_RIGHT 1 - -MN908947.3 1245 1266 SARS-CoV-2_5_LEFT 1 + -MN908947.3 1337 1362 SARS-CoV-2_4_RIGHT 2 - -MN908947.3 1540 1562 SARS-CoV-2_6_LEFT 2 + -MN908947.3 1623 1650 SARS-CoV-2_5_RIGHT 1 - -MN908947.3 1851 1875 SARS-CoV-2_7_LEFT 1 + -MN908947.3 1925 1948 SARS-CoV-2_6_RIGHT 2 - -MN908947.3 2154 2180 SARS-CoV-2_8_LEFT 2 + -MN908947.3 2228 2250 SARS-CoV-2_7_RIGHT 1 - -MN908947.3 2483 2508 SARS-CoV-2_9_LEFT 1 + -MN908947.3 2544 2571 SARS-CoV-2_8_RIGHT 2 - -MN908947.3 2780 2813 SARS-CoV-2_10_LEFT_alt1 2 + -MN908947.3 2826 2850 SARS-CoV-2_10_LEFT 2 + -MN908947.3 2861 2885 SARS-CoV-2_9_RIGHT 1 - -MN908947.3 3078 3102 SARS-CoV-2_11_LEFT 1 + -MN908947.3 3156 3177 SARS-CoV-2_10_RIGHT_alt1 2 - -MN908947.3 3183 3210 SARS-CoV-2_10_RIGHT 2 - -MN908947.3 3390 3412 SARS-CoV-2_12_LEFT 2 + -MN908947.3 3470 3492 SARS-CoV-2_11_RIGHT 1 - -MN908947.3 3683 3705 SARS-CoV-2_13_LEFT 1 + -MN908947.3 3769 3794 SARS-CoV-2_12_RIGHT 2 - -MN908947.3 3992 4018 SARS-CoV-2_14_LEFT 2 + -MN908947.3 4067 4093 SARS-CoV-2_13_RIGHT 1 - -MN908947.3 4312 4339 SARS-CoV-2_15_LEFT 1 + -MN908947.3 4387 4409 SARS-CoV-2_14_RIGHT 2 - -MN908947.3 4620 4648 SARS-CoV-2_16_LEFT 2 + -MN908947.3 4685 4710 SARS-CoV-2_15_RIGHT 1 - -MN908947.3 4923 4953 SARS-CoV-2_17_LEFT 1 + -MN908947.3 4995 5017 SARS-CoV-2_16_RIGHT 2 - -MN908947.3 5230 5259 SARS-CoV-2_18_LEFT 2 + -MN908947.3 5302 5331 SARS-CoV-2_17_RIGHT 1 - -MN908947.3 5561 5584 SARS-CoV-2_19_LEFT 1 + -MN908947.3 5620 5643 SARS-CoV-2_18_RIGHT 2 - -MN908947.3 5867 5894 SARS-CoV-2_20_LEFT 2 + -MN908947.3 5932 5957 SARS-CoV-2_19_RIGHT 1 - -MN908947.3 6184 6210 SARS-CoV-2_21_LEFT 1 + -MN908947.3 6247 6272 SARS-CoV-2_20_RIGHT 2 - -MN908947.3 6478 6507 SARS-CoV-2_22_LEFT 2 + -MN908947.3 6553 6582 SARS-CoV-2_21_RIGHT 1 - -MN908947.3 6747 6776 SARS-CoV-2_23_LEFT 1 + -MN908947.3 6859 6885 SARS-CoV-2_22_RIGHT 2 - -MN908947.3 7057 7084 SARS-CoV-2_24_LEFT 2 + -MN908947.3 7122 7148 SARS-CoV-2_23_RIGHT 1 - -MN908947.3 7127 7156 SARS-CoV-2_23_RIGHT_alt1 1 - -MN908947.3 7381 7403 SARS-CoV-2_25_LEFT 1 + -MN908947.3 7440 7467 SARS-CoV-2_24_RIGHT 2 - -MN908947.3 7672 7695 SARS-CoV-2_26_LEFT 2 + -MN908947.3 7747 7770 SARS-CoV-2_25_RIGHT 1 - -MN908947.3 7997 8019 SARS-CoV-2_27_LEFT 1 + -MN908947.3 8063 8092 SARS-CoV-2_26_RIGHT 2 - -MN908947.3 8304 8326 SARS-CoV-2_28_LEFT 2 + -MN908947.3 8367 8392 SARS-CoV-2_27_RIGHT_alt1 1 - -MN908947.3 8370 8395 SARS-CoV-2_27_RIGHT 1 - -MN908947.3 8596 8619 SARS-CoV-2_29_LEFT 1 + -MN908947.3 8691 8714 SARS-CoV-2_28_RIGHT 2 - -MN908947.3 8919 8944 SARS-CoV-2_30_LEFT 2 + -MN908947.3 8990 9013 SARS-CoV-2_29_RIGHT 1 - -MN908947.3 9168 9192 SARS-CoV-2_31_LEFT 1 + -MN908947.3 9306 9329 SARS-CoV-2_30_RIGHT 2 - -MN908947.3 9470 9497 SARS-CoV-2_32_LEFT 2 + -MN908947.3 9535 9564 SARS-CoV-2_31_RIGHT 1 - -MN908947.3 9782 9805 SARS-CoV-2_33_LEFT 1 + -MN908947.3 9842 9866 SARS-CoV-2_32_RIGHT 2 - -MN908947.3 10076 10099 SARS-CoV-2_34_LEFT 2 + -MN908947.3 10150 10176 SARS-CoV-2_33_RIGHT 1 - -MN908947.3 10393 10419 SARS-CoV-2_35_LEFT 1 + -MN908947.3 10465 10491 SARS-CoV-2_34_RIGHT 2 - -MN908947.3 10713 10742 SARS-CoV-2_36_LEFT 2 + -MN908947.3 10785 10810 SARS-CoV-2_35_RIGHT 1 - -MN908947.3 11000 11023 SARS-CoV-2_37_LEFT 1 + -MN908947.3 11092 11116 SARS-CoV-2_36_RIGHT 2 - -MN908947.3 11305 11330 SARS-CoV-2_38_LEFT 2 + -MN908947.3 11388 11414 SARS-CoV-2_37_RIGHT 1 - -MN908947.3 11624 11651 SARS-CoV-2_39_LEFT 1 + -MN908947.3 11689 11720 SARS-CoV-2_38_RIGHT 2 - -MN908947.3 11937 11963 SARS-CoV-2_40_LEFT 2 + -MN908947.3 12011 12033 SARS-CoV-2_39_RIGHT 1 - -MN908947.3 12234 12255 SARS-CoV-2_41_LEFT 1 + -MN908947.3 12317 12339 SARS-CoV-2_40_RIGHT 2 - -MN908947.3 12519 12546 SARS-CoV-2_42_LEFT 2 + -MN908947.3 12618 12643 SARS-CoV-2_41_RIGHT 1 - -MN908947.3 12831 12856 SARS-CoV-2_43_LEFT 1 + -MN908947.3 12895 12920 SARS-CoV-2_42_RIGHT 2 - -MN908947.3 13124 13148 SARS-CoV-2_44_LEFT 2 + -MN908947.3 13218 13240 SARS-CoV-2_43_RIGHT 1 - -MN908947.3 13463 13485 SARS-CoV-2_45_LEFT 1 + -MN908947.3 13506 13528 SARS-CoV-2_44_RIGHT 2 - -MN908947.3 13752 13775 SARS-CoV-2_46_LEFT 2 + -MN908947.3 13833 13859 SARS-CoV-2_45_RIGHT 1 - -MN908947.3 14045 14075 SARS-CoV-2_47_LEFT 1 + -MN908947.3 14120 14144 SARS-CoV-2_46_RIGHT 2 - -MN908947.3 14338 14362 SARS-CoV-2_48_LEFT 2 + -MN908947.3 14428 14457 SARS-CoV-2_47_RIGHT 1 - -MN908947.3 14647 14674 SARS-CoV-2_49_LEFT 1 + -MN908947.3 14717 14743 SARS-CoV-2_48_RIGHT 2 - -MN908947.3 14953 14983 SARS-CoV-2_50_LEFT 2 + -MN908947.3 15023 15050 SARS-CoV-2_49_RIGHT 1 - -MN908947.3 15214 15237 SARS-CoV-2_51_LEFT 1 + -MN908947.3 15336 15358 SARS-CoV-2_50_RIGHT 2 - -MN908947.3 15535 15557 SARS-CoV-2_52_LEFT 2 + -MN908947.3 15596 15619 SARS-CoV-2_51_RIGHT 1 - -MN908947.3 15855 15881 SARS-CoV-2_53_LEFT 1 + -MN908947.3 15917 15941 SARS-CoV-2_52_RIGHT 2 - -MN908947.3 16112 16137 SARS-CoV-2_54_LEFT 2 + -MN908947.3 16239 16260 SARS-CoV-2_53_RIGHT 1 - -MN908947.3 16386 16408 SARS-CoV-2_55_LEFT 1 + -MN908947.3 16483 16508 SARS-CoV-2_54_RIGHT 2 - -MN908947.3 16692 16714 SARS-CoV-2_56_LEFT 2 + -MN908947.3 16767 16796 SARS-CoV-2_55_RIGHT 1 - -MN908947.3 16986 17013 SARS-CoV-2_57_LEFT 1 + -MN908947.3 17082 17105 SARS-CoV-2_56_RIGHT 2 - -MN908947.3 17323 17345 SARS-CoV-2_58_LEFT 2 + -MN908947.3 17381 17405 SARS-CoV-2_57_RIGHT 1 - -MN908947.3 17615 17642 SARS-CoV-2_59_LEFT 1 + -MN908947.3 17688 17711 SARS-CoV-2_58_RIGHT 2 - -MN908947.3 17911 17939 SARS-CoV-2_60_LEFT 2 + -MN908947.3 17997 18022 SARS-CoV-2_59_RIGHT 1 - -MN908947.3 18244 18267 SARS-CoV-2_61_LEFT 1 + -MN908947.3 18307 18328 SARS-CoV-2_60_RIGHT 2 - -MN908947.3 18550 18578 SARS-CoV-2_62_LEFT 2 + -MN908947.3 18624 18652 SARS-CoV-2_61_RIGHT 1 - -MN908947.3 18869 18891 SARS-CoV-2_63_LEFT 1 + -MN908947.3 18936 18961 SARS-CoV-2_62_RIGHT 2 - -MN908947.3 19183 19208 SARS-CoV-2_64_LEFT 2 + -MN908947.3 19252 19277 SARS-CoV-2_63_RIGHT 1 - -MN908947.3 19485 19513 SARS-CoV-2_65_LEFT 1 + -MN908947.3 19558 19586 SARS-CoV-2_64_RIGHT 2 - -MN908947.3 19810 19836 SARS-CoV-2_66_LEFT 2 + -MN908947.3 19877 19901 SARS-CoV-2_65_RIGHT 1 - -MN908947.3 20090 20117 SARS-CoV-2_67_LEFT 1 + -MN908947.3 20186 20216 SARS-CoV-2_66_RIGHT 2 - -MN908947.3 20377 20405 SARS-CoV-2_68_LEFT 2 + -MN908947.3 20472 20497 SARS-CoV-2_67_RIGHT 1 - -MN908947.3 20677 20699 SARS-CoV-2_69_LEFT 1 + -MN908947.3 20766 20792 SARS-CoV-2_68_RIGHT 2 - -MN908947.3 20988 21013 SARS-CoV-2_70_LEFT 2 + -MN908947.3 21050 21080 SARS-CoV-2_69_RIGHT 1 - -MN908947.3 21294 21316 SARS-CoV-2_71_LEFT 1 + -MN908947.3 21358 21387 SARS-CoV-2_70_RIGHT 2 - -MN908947.3 21532 21561 SARS-CoV-2_72_LEFT 2 + -MN908947.3 21675 21700 SARS-CoV-2_71_RIGHT 1 - -MN908947.3 21865 21889 SARS-CoV-2_73_LEFT 1 + -MN908947.3 21904 21933 SARS-CoV-2_72_RIGHT 2 - -MN908947.3 22091 22113 SARS-CoV-2_74_LEFT 2 + -MN908947.3 22247 22274 SARS-CoV-2_73_RIGHT 1 - -MN908947.3 22402 22428 SARS-CoV-2_75_LEFT 1 + -MN908947.3 22474 22503 SARS-CoV-2_74_RIGHT 2 - -MN908947.3 22648 22677 SARS-CoV-2_76_LEFT 2 + -MN908947.3 22742 22774 SARS-CoV-2_76_LEFT_alt1 2 + -MN908947.3 22785 22805 SARS-CoV-2_75_RIGHT 1 - -MN908947.3 22944 22974 SARS-CoV-2_77_LEFT 1 + -MN908947.3 23028 23057 SARS-CoV-2_76_RIGHT 2 - -MN908947.3 23120 23141 SARS-CoV-2_76_RIGHT_alt1 2 - -MN908947.3 23219 23246 SARS-CoV-2_78_LEFT 2 + -MN908947.3 23327 23351 SARS-CoV-2_77_RIGHT 1 - -MN908947.3 23553 23575 SARS-CoV-2_79_LEFT 1 + -MN908947.3 23611 23635 SARS-CoV-2_78_RIGHT 2 - -MN908947.3 23853 23876 SARS-CoV-2_80_LEFT 2 + -MN908947.3 23914 23944 SARS-CoV-2_79_RIGHT_alt1 1 - -MN908947.3 23927 23955 SARS-CoV-2_79_RIGHT 1 - -MN908947.3 24171 24194 SARS-CoV-2_81_LEFT 1 + -MN908947.3 24233 24258 SARS-CoV-2_80_RIGHT 2 - -MN908947.3 24426 24448 SARS-CoV-2_82_LEFT 2 + -MN908947.3 24545 24567 SARS-CoV-2_81_RIGHT 1 - -MN908947.3 24750 24772 SARS-CoV-2_83_LEFT 1 + -MN908947.3 24814 24836 SARS-CoV-2_82_RIGHT 2 - -MN908947.3 25051 25076 SARS-CoV-2_84_LEFT 2 + -MN908947.3 25122 25150 SARS-CoV-2_83_RIGHT 1 - -MN908947.3 25331 25353 SARS-CoV-2_85_LEFT 1 + -MN908947.3 25438 25461 SARS-CoV-2_84_RIGHT 2 - -MN908947.3 25645 25672 SARS-CoV-2_86_LEFT 2 + -MN908947.3 25711 25740 SARS-CoV-2_85_RIGHT 1 - -MN908947.3 25951 25979 SARS-CoV-2_87_LEFT 1 + -MN908947.3 26026 26050 SARS-CoV-2_86_RIGHT 2 - -MN908947.3 26242 26268 SARS-CoV-2_88_LEFT_alt1 2 + -MN908947.3 26255 26277 SARS-CoV-2_88_LEFT 2 + -MN908947.3 26338 26360 SARS-CoV-2_87_RIGHT 1 - -MN908947.3 26564 26587 SARS-CoV-2_89_LEFT 1 + -MN908947.3 26592 26621 SARS-CoV-2_89_LEFT_alt1 1 + -MN908947.3 26635 26661 SARS-CoV-2_88_RIGHT 2 - -MN908947.3 26873 26895 SARS-CoV-2_90_LEFT 2 + -MN908947.3 26956 26979 SARS-CoV-2_89_RIGHT 1 - -MN908947.3 26966 26991 SARS-CoV-2_89_RIGHT_alt1 1 - -MN908947.3 27152 27177 SARS-CoV-2_91_LEFT 1 + -MN908947.3 27218 27251 SARS-CoV-2_90_RIGHT_alt1 2 - -MN908947.3 27256 27283 SARS-CoV-2_90_RIGHT 2 - -MN908947.3 27447 27473 SARS-CoV-2_92_LEFT 2 + -MN908947.3 27534 27560 SARS-CoV-2_91_RIGHT 1 - -MN908947.3 27700 27726 SARS-CoV-2_93_LEFT 1 + -MN908947.3 27826 27855 SARS-CoV-2_92_RIGHT 2 - -MN908947.3 27996 28021 SARS-CoV-2_94_LEFT 2 + -MN908947.3 28082 28104 SARS-CoV-2_93_RIGHT 1 - -MN908947.3 28190 28214 SARS-CoV-2_95_LEFT 1 + -MN908947.3 28394 28416 SARS-CoV-2_94_RIGHT 2 - -MN908947.3 28512 28536 SARS-CoV-2_96_LEFT 2 + -MN908947.3 28572 28598 SARS-CoV-2_95_RIGHT 1 - -MN908947.3 28827 28849 SARS-CoV-2_97_LEFT 1 + -MN908947.3 28893 28914 SARS-CoV-2_96_RIGHT 2 - -MN908947.3 29136 29161 SARS-CoV-2_98_LEFT 2 + -MN908947.3 29206 29227 SARS-CoV-2_97_RIGHT 1 - -MN908947.3 29452 29475 SARS-CoV-2_99_LEFT 1 + -MN908947.3 29512 29534 SARS-CoV-2_98_RIGHT 2 - -MN908947.3 29827 29854 SARS-CoV-2_99_RIGHT 1 - diff --git a/test/data/primer-schemes/eden/v1/info.yml b/test/data/primer-schemes/eden/v1/info.yml deleted file mode 100644 index f5e0626..0000000 --- a/test/data/primer-schemes/eden/v1/info.yml +++ /dev/null @@ -1,19 +0,0 @@ -schema_version: 0.9.0 -name: eden-v1 -organism: sars-cov-2 -aliases: -- sydney -developers: -- person_name: John-Sebastian Eden - orcid: 0000-0003-1374-3551 -- person_name: Eby Sim - orcid: 0000-0002-3716-7344 -vendors: [] -amplicon_size: 2500 -repository_url: https://github.com/pha4ge/primer-schemes/tree/main/sars-cov-2/eden/v1 -citations: -- https://www.protocols.io/view/sars-cov-2-genome-sequencing-using-long-pooled-amp-kxygxeob4v8j/v1 -notes: -- Protocol includes addendum for ONT sequencing -primer_checksum: primaschema:9f9c80501b744d15 -reference_checksum: primaschema:7d5621cd3b3e498d diff --git a/test/data/primer-schemes/eden/v1/primer.bed b/test/data/primer-schemes/eden/v1/primer.bed deleted file mode 100644 index 521b3ed..0000000 --- a/test/data/primer-schemes/eden/v1/primer.bed +++ /dev/null @@ -1,28 +0,0 @@ -MN908947.3 31 55 SARS2_A1F_31 1 + CCAACCAACTTTCGATCTCTTGTA -MN908947.3 2569 2593 SARS2_A1R_2569 1 - AGCTTCAACAGCTTCACTAGTAGG -MN908947.3 4295 4322 SARS2_A2F_4295 2 + CAGTGCTTAAAAAGTGTAAAAGTGCCT -MN908947.3 6847 6874 SARS2_A2R_6847 2 - AACAGTATTCTTTGCTATAGTAGTCGG -MN908947.3 8596 8620 SARS2_A3F_8596 1 + CTTGTGTTCCTTTTTGTTGCTGCT -MN908947.3 11049 11075 SARS2_A3R_11049 1 - AGAACAAAGACCATTGAGTACTCTGG -MN908947.3 12711 12733 SARS2_A4F_12711 2 + ACGACAGATGTCTTGTGCTGCC -MN908947.3 15225 15247 SARS2_A4R_15225 2 - TTAACATGTTGTGCCAACCACC -MN908947.3 16847 16872 SARS2_A5F_16847 1 + CTATGGTGATGCTGTTGTTTACCGA -MN908947.3 19254 19279 SARS2_A5R_19254 1 - AACCAGGCAAGTTAAGGTTAGATAG -MN908947.3 21358 21387 SARS2_A6F_21358 2 + CAAATCCAATTCAGTTGTCTTCCTATTCT -MN908947.3 23823 23848 SARS2_A6R_23823 2 - TTGTGTACAAAAACTGCCATATTGC -MN908947.3 25602 25624 SARS2_A7F_25602 1 + CTAGCACTCTCCAAGGGTGTTC -MN908947.3 28146 28173 SARS2_A7R_28146 1 - TAGGTTCCTGGCAATTAATTGTAAAAG -MN908947.3 1876 1898 SARS2_B1F_1876 2 + TCAGAGGCTGCTCGTGTTGTAC -MN908947.3 4429 4451 SARS2_B1R_4429 2 - TAGTTTCCACACAGACAGGCAT -MN908947.3 6287 6311 SARS2_B2F_6287 1 + GGTGTATACGTTGTCTTTGGAGCA -MN908947.3 8828 8852 SARS2_B2R_8828 1 - CCACTTCTCTTGTTATGACTGCAG -MN908947.3 10363 10385 SARS2_B3F_10363 2 + GTTCGCATTCAACCAGGACAGA -MN908947.3 12780 12803 SARS2_B3R_12780 2 - ACCTACCTCCCTTTGTTGTGTTG -MN908947.3 14546 14571 SARS2_B4F_14546 1 + GGAATTACTTGTGTATGCTGCTGAC -MN908947.3 17131 17153 SARS2_B4R_17131 1 - TACACTATGCGAGCAGAAGGGT -MN908947.3 18897 18919 SARS2_B5F_18897 2 + GTTAAGCGTGTTGACTGGACTA -MN908947.3 21428 21456 SARS2_B5R_21428 2 - TTGACCTTCTTTTAAAGACATAACAGCA -MN908947.3 23123 23145 SARS2_B6F_23123 1 + CAGCAACTGTTTGTGGACCTAA -MN908947.3 25647 25674 SARS2_B6R_25647 1 - AAGGTGTGAGTAAACTGTTACAAACAA -MN908947.3 27447 27472 SARS2_B7F_27447 2 + CACTACCAAGAGTGTGTTAGAGGTA -MN908947.3 29837 29867 SARS2_B7R_29837 2 - ATTCTCCTAAGAAGCTATTAAAATCACATG diff --git a/test/data/primer-schemes/eden/v1/scheme.bed b/test/data/primer-schemes/eden/v1/scheme.bed deleted file mode 100644 index 8cb4f62..0000000 --- a/test/data/primer-schemes/eden/v1/scheme.bed +++ /dev/null @@ -1,28 +0,0 @@ -MN908947.3 31 55 SARS2_A1F_31 1 + -MN908947.3 2569 2593 SARS2_A1R_2569 1 - -MN908947.3 4295 4322 SARS2_A2F_4295 2 + -MN908947.3 6847 6874 SARS2_A2R_6847 2 - -MN908947.3 8596 8620 SARS2_A3F_8596 1 + -MN908947.3 11049 11075 SARS2_A3R_11049 1 - -MN908947.3 12711 12733 SARS2_A4F_12711 2 + -MN908947.3 15225 15247 SARS2_A4R_15225 2 - -MN908947.3 16847 16872 SARS2_A5F_16847 1 + -MN908947.3 19254 19279 SARS2_A5R_19254 1 - -MN908947.3 21358 21387 SARS2_A6F_21358 2 + -MN908947.3 23823 23848 SARS2_A6R_23823 2 - -MN908947.3 25602 25624 SARS2_A7F_25602 1 + -MN908947.3 28146 28173 SARS2_A7R_28146 1 - -MN908947.3 1876 1898 SARS2_B1F_1876 2 + -MN908947.3 4429 4451 SARS2_B1R_4429 2 - -MN908947.3 6287 6311 SARS2_B2F_6287 1 + -MN908947.3 8828 8852 SARS2_B2R_8828 1 - -MN908947.3 10363 10385 SARS2_B3F_10363 2 + -MN908947.3 12780 12803 SARS2_B3R_12780 2 - -MN908947.3 14546 14571 SARS2_B4F_14546 1 + -MN908947.3 17131 17153 SARS2_B4R_17131 1 - -MN908947.3 18897 18919 SARS2_B5F_18897 2 + -MN908947.3 21428 21456 SARS2_B5R_21428 2 - -MN908947.3 23123 23145 SARS2_B6F_23123 1 + -MN908947.3 25647 25674 SARS2_B6R_25647 1 - -MN908947.3 27447 27472 SARS2_B7F_27447 2 + -MN908947.3 29837 29867 SARS2_B7R_29837 2 - diff --git a/test/data/primer-schemes/midnight/v1/primer.bed b/test/data/primer-schemes/midnight/v1/primer.bed deleted file mode 100644 index a102da9..0000000 --- a/test/data/primer-schemes/midnight/v1/primer.bed +++ /dev/null @@ -1,58 +0,0 @@ -MN908947.3 30 54 SARS-CoV-2_1_LEFT 1 + ACCAACCAACTTTCGATCTCTTGT -MN908947.3 1183 1205 SARS-CoV-2_1_RIGHT 1 - GGTTGCATTCATTTGGTGACGC -MN908947.3 1100 1128 SARS-CoV-2_2_LEFT 2 + CCATAATCAAGACTATTCAACCAAGGGT -MN908947.3 2244 2266 SARS-CoV-2_2_RIGHT 2 - ACAGGTGACAATTTGTCCACCG -MN908947.3 2153 2179 SARS-CoV-2_3_LEFT 1 + GGCTTGAAGAGAAGTTTAAGGAAGGT -MN908947.3 3235 3257 SARS-CoV-2_3_RIGHT 1 - GATTGTCCTCACTGCCGTCTTG -MN908947.3 3144 3166 SARS-CoV-2_4_LEFT 2 + GGAATTTGGTGCCACTTCTGCT -MN908947.3 4240 4262 SARS-CoV-2_4_RIGHT 2 - CCTGACCCGGGTAAGTGGTTAT -MN908947.3 4167 4189 SARS-CoV-2_5_LEFT 1 + ACCTACTAAAAAGGCTGGTGGC -MN908947.3 5337 5359 SARS-CoV-2_5_RIGHT 1 - AGCATCTTGTAGAGCAGGTGGA -MN908947.3 5257 5286 SARS-CoV-2_6_LEFT 2 + ACTTCTATTAAATGGGCAGATAACAACTG -MN908947.3 6358 6380 SARS-CoV-2_6_RIGHT 2 - GATTATCCATTCCCTGCGCGTC -MN908947.3 6283 6307 SARS-CoV-2_7_LEFT 1 + ACCTGGTGTATACGTTGTCTTTGG -MN908947.3 7379 7401 SARS-CoV-2_7_RIGHT 1 - GCTGAAATCGGGGCCATTTGTA -MN908947.3 7298 7328 SARS-CoV-2_8_LEFT 2 + CAATCATGCAATTGTTTTTCAGCTATTTTG -MN908947.3 8363 8385 SARS-CoV-2_8_RIGHT 2 - TGACTTTTTGCTACCTGCGCAT -MN908947.3 8253 8282 SARS-CoV-2_9_LEFT 1 + AGAAGTTACTGGCGATAGTTGTAATAACT -MN908947.3 9378 9400 SARS-CoV-2_9_RIGHT 1 - TGCTGATATGTCCAAAGCACCA -MN908947.3 9303 9327 SARS-CoV-2_10_LEFT 2 + TTTACCAGGAGTTTTCTGTGGTGT -MN908947.3 10429 10451 SARS-CoV-2_10_RIGHT 2 - TGGGCCTCATAGCACATTGGTA -MN908947.3 10343 10370 SARS-CoV-2_11_LEFT 1 + AGACACCTAAGTATAAGTTTGTTCGCA -MN908947.3 11447 11469 SARS-CoV-2_11_RIGHT 1 - GCCCACATGGAAATGGCTTGAT -MN908947.3 11372 11394 SARS-CoV-2_12_LEFT 2 + ATGGTGCTAGGAGAGTGTGGAC -MN908947.3 12538 12560 SARS-CoV-2_12_RIGHT 2 - GGATTTCCCACAATGCTGATGC -MN908947.3 12450 12473 SARS-CoV-2_13_LEFT 1 + ACCTCTTACAACAGCAGCCAAAC -MN908947.3 13599 13621 SARS-CoV-2_13_RIGHT 1 - CGTCCTTTTCTTGGAAGCGACA -MN908947.3 13509 13532 SARS-CoV-2_14_LEFT 2 + ACAGGCACTAGTACTGATGTCGT -MN908947.3 14619 14641 SARS-CoV-2_14_RIGHT 2 - GTGCAGCTACTGAAAAGCACGT -MN908947.3 14540 14568 SARS-CoV-2_15_LEFT 1 + TTTTAAGGAATTACTTGTGTATGCTGCT -MN908947.3 15713 15735 SARS-CoV-2_15_RIGHT 1 - ACACACAACAGCATCGTCAGAG -MN908947.3 15608 15634 SARS-CoV-2_16_LEFT 2 + ACAACACAGACTTTATGAGTGTCTCT -MN908947.3 16698 16720 SARS-CoV-2_16_RIGHT 2 - CTCTGTCAGACAGCACTTCACG -MN908947.3 16624 16647 SARS-CoV-2_17_LEFT 1 + TCAAGCTTTTTGCAGCAGAAACG -MN908947.3 17732 17754 SARS-CoV-2_17_RIGHT 1 - CCAAGCAGGGTTACGTGTAAGG -MN908947.3 17622 17649 SARS-CoV-2_18_LEFT 2 + GCACATAAAGACAAATCAGCTCAATGC -MN908947.3 18684 18706 SARS-CoV-2_18_RIGHT 2 - TGTCTGAAGCAGTGGAAAAGCA -MN908947.3 18596 18618 SARS-CoV-2_19_LEFT 1 + GGCACATGGCTTTGAGTTGACA -MN908947.3 19655 19678 SARS-CoV-2_19_RIGHT 1 - CCTGTTGTCCATCAAAGTGTCCC -MN908947.3 19574 19604 SARS-CoV-2_20_LEFT 2 + ACAATTTGATACTTATAACCTCTGGAACAC -MN908947.3 20676 20698 SARS-CoV-2_20_RIGHT 2 - GATTAGGCATAGCAACACCCGG -MN908947.3 20553 20581 SARS-CoV-2_21_LEFT 1 + TCTGTAGTTTCTAAGGTTGTCAAAGTGA -MN908947.3 21620 21642 SARS-CoV-2_21_RIGHT 1 - GCAGGGGGTAATTGAGTTCTGG -MN908947.3 21532 21562 SARS-CoV-2_22_LEFT 2 + GTGATGTTCTTGTTAACAACTAAACGAACA -MN908947.3 22590 22612 SARS-CoV-2_22_RIGHT 2 - AACAGATGCAAATCTGGTGGCG -MN908947.3 22511 22537 SARS-CoV-2_23_LEFT 1 + ACTTTAGAGTCCAACCAACAGAATCT -MN908947.3 23609 23631 SARS-CoV-2_23_RIGHT 1 - TGACTAGCTACACTACGTGCCC -MN908947.3 23518 23544 SARS-CoV-2_24_LEFT 2 + GCTGAACATGTCAACAACTCATATGA -MN908947.3 24714 24736 SARS-CoV-2_24_RIGHT 2 - ATGAGGTGCTGACTGAGGGAAG -MN908947.3 24633 24658 SARS-CoV-2_25_LEFT 1 + TGCTGCTACTAAAATGTCAGAGTGT -MN908947.3 25768 25790 SARS-CoV-2_25_RIGHT 1 - CATTTCCAGCAAAGCCAAAGCC -MN908947.3 25690 25712 SARS-CoV-2_26_LEFT 2 + GCCTTGAAGCCCCTTTTCTCTA -MN908947.3 26835 26857 SARS-CoV-2_26_RIGHT 2 - AATGACCACATGGAACGCGTAC -MN908947.3 26744 26766 SARS-CoV-2_27_LEFT 1 + TGGATCACCGGTGGAATTGCTA -MN908947.3 27872 27894 SARS-CoV-2_27_RIGHT 1 - TGTTCGTTTAGGCGTGACAAGT -MN908947.3 27784 27808 SARS-CoV-2_28_LEFT 2 + TTTGTGCTTTTTAGCCTTTCTGCT -MN908947.3 28985 29007 SARS-CoV-2_28_RIGHT 2 - GTTTGGCCTTGTTGTTGTTGGC -MN908947.3 28677 28699 SARS-CoV-2_29_LEFT 1 + TGAGGGAGCCTTGAATACACCA -MN908947.3 29768 29790 SARS-CoV-2_29_RIGHT 1 - TAGGCAGCTCTCCCTAGCATTG diff --git a/test/data/primer-schemes/midnight/v1/scheme.bed b/test/data/primer-schemes/midnight/v1/scheme.bed deleted file mode 100644 index 6cafe12..0000000 --- a/test/data/primer-schemes/midnight/v1/scheme.bed +++ /dev/null @@ -1,58 +0,0 @@ -MN908947.3 30 54 SARS-CoV-2_1_LEFT 1 + -MN908947.3 1183 1205 SARS-CoV-2_1_RIGHT 1 - -MN908947.3 1100 1128 SARS-CoV-2_2_LEFT 2 + -MN908947.3 2244 2266 SARS-CoV-2_2_RIGHT 2 - -MN908947.3 2153 2179 SARS-CoV-2_3_LEFT 1 + -MN908947.3 3235 3257 SARS-CoV-2_3_RIGHT 1 - -MN908947.3 3144 3166 SARS-CoV-2_4_LEFT 2 + -MN908947.3 4240 4262 SARS-CoV-2_4_RIGHT 2 - -MN908947.3 4167 4189 SARS-CoV-2_5_LEFT 1 + -MN908947.3 5337 5359 SARS-CoV-2_5_RIGHT 1 - -MN908947.3 5257 5286 SARS-CoV-2_6_LEFT 2 + -MN908947.3 6358 6380 SARS-CoV-2_6_RIGHT 2 - -MN908947.3 6283 6307 SARS-CoV-2_7_LEFT 1 + -MN908947.3 7379 7401 SARS-CoV-2_7_RIGHT 1 - -MN908947.3 7298 7328 SARS-CoV-2_8_LEFT 2 + -MN908947.3 8363 8385 SARS-CoV-2_8_RIGHT 2 - -MN908947.3 8253 8282 SARS-CoV-2_9_LEFT 1 + -MN908947.3 9378 9400 SARS-CoV-2_9_RIGHT 1 - -MN908947.3 9303 9327 SARS-CoV-2_10_LEFT 2 + -MN908947.3 10429 10451 SARS-CoV-2_10_RIGHT 2 - -MN908947.3 10343 10370 SARS-CoV-2_11_LEFT 1 + -MN908947.3 11447 11469 SARS-CoV-2_11_RIGHT 1 - -MN908947.3 11372 11394 SARS-CoV-2_12_LEFT 2 + -MN908947.3 12538 12560 SARS-CoV-2_12_RIGHT 2 - -MN908947.3 12450 12473 SARS-CoV-2_13_LEFT 1 + -MN908947.3 13599 13621 SARS-CoV-2_13_RIGHT 1 - -MN908947.3 13509 13532 SARS-CoV-2_14_LEFT 2 + -MN908947.3 14619 14641 SARS-CoV-2_14_RIGHT 2 - -MN908947.3 14540 14568 SARS-CoV-2_15_LEFT 1 + -MN908947.3 15713 15735 SARS-CoV-2_15_RIGHT 1 - -MN908947.3 15608 15634 SARS-CoV-2_16_LEFT 2 + -MN908947.3 16698 16720 SARS-CoV-2_16_RIGHT 2 - -MN908947.3 16624 16647 SARS-CoV-2_17_LEFT 1 + -MN908947.3 17732 17754 SARS-CoV-2_17_RIGHT 1 - -MN908947.3 17622 17649 SARS-CoV-2_18_LEFT 2 + -MN908947.3 18684 18706 SARS-CoV-2_18_RIGHT 2 - -MN908947.3 18596 18618 SARS-CoV-2_19_LEFT 1 + -MN908947.3 19655 19678 SARS-CoV-2_19_RIGHT 1 - -MN908947.3 19574 19604 SARS-CoV-2_20_LEFT 2 + -MN908947.3 20676 20698 SARS-CoV-2_20_RIGHT 2 - -MN908947.3 20553 20581 SARS-CoV-2_21_LEFT 1 + -MN908947.3 21620 21642 SARS-CoV-2_21_RIGHT 1 - -MN908947.3 21532 21562 SARS-CoV-2_22_LEFT 2 + -MN908947.3 22590 22612 SARS-CoV-2_22_RIGHT 2 - -MN908947.3 22511 22537 SARS-CoV-2_23_LEFT 1 + -MN908947.3 23609 23631 SARS-CoV-2_23_RIGHT 1 - -MN908947.3 23518 23544 SARS-CoV-2_24_LEFT 2 + -MN908947.3 24714 24736 SARS-CoV-2_24_RIGHT 2 - -MN908947.3 24633 24658 SARS-CoV-2_25_LEFT 1 + -MN908947.3 25768 25790 SARS-CoV-2_25_RIGHT 1 - -MN908947.3 25690 25712 SARS-CoV-2_26_LEFT 2 + -MN908947.3 26835 26857 SARS-CoV-2_26_RIGHT 2 - -MN908947.3 26744 26766 SARS-CoV-2_27_LEFT 1 + -MN908947.3 27872 27894 SARS-CoV-2_27_RIGHT 1 - -MN908947.3 27784 27808 SARS-CoV-2_28_LEFT 2 + -MN908947.3 28985 29007 SARS-CoV-2_28_RIGHT 2 - -MN908947.3 28677 28699 SARS-CoV-2_29_LEFT 1 + -MN908947.3 29768 29790 SARS-CoV-2_29_RIGHT 1 - diff --git a/test/data/primer-schemes/midnight/v2/primer.bed b/test/data/primer-schemes/midnight/v2/primer.bed deleted file mode 100644 index f223c84..0000000 --- a/test/data/primer-schemes/midnight/v2/primer.bed +++ /dev/null @@ -1,59 +0,0 @@ -MN908947.3 30 54 SARS-CoV-2_1_LEFT 1 + ACCAACCAACTTTCGATCTCTTGT -MN908947.3 1183 1205 SARS-CoV-2_1_RIGHT 1 - GGTTGCATTCATTTGGTGACGC -MN908947.3 1100 1128 SARS-CoV-2_2_LEFT 2 + CCATAATCAAGACTATTCAACCAAGGGT -MN908947.3 2244 2266 SARS-CoV-2_2_RIGHT 2 - ACAGGTGACAATTTGTCCACCG -MN908947.3 2153 2179 SARS-CoV-2_3_LEFT 1 + GGCTTGAAGAGAAGTTTAAGGAAGGT -MN908947.3 3235 3257 SARS-CoV-2_3_RIGHT 1 - GATTGTCCTCACTGCCGTCTTG -MN908947.3 3144 3166 SARS-CoV-2_4_LEFT 2 + GGAATTTGGTGCCACTTCTGCT -MN908947.3 4240 4262 SARS-CoV-2_4_RIGHT 2 - CCTGACCCGGGTAAGTGGTTAT -MN908947.3 4167 4189 SARS-CoV-2_5_LEFT 1 + ACCTACTAAAAAGGCTGGTGGC -MN908947.3 5337 5359 SARS-CoV-2_5_RIGHT 1 - AGCATCTTGTAGAGCAGGTGGA -MN908947.3 5257 5286 SARS-CoV-2_6_LEFT 2 + ACTTCTATTAAATGGGCAGATAACAACTG -MN908947.3 6358 6380 SARS-CoV-2_6_RIGHT 2 - GATTATCCATTCCCTGCGCGTC -MN908947.3 6283 6307 SARS-CoV-2_7_LEFT 1 + ACCTGGTGTATACGTTGTCTTTGG -MN908947.3 7379 7401 SARS-CoV-2_7_RIGHT 1 - GCTGAAATCGGGGCCATTTGTA -MN908947.3 7298 7328 SARS-CoV-2_8_LEFT 2 + CAATCATGCAATTGTTTTTCAGCTATTTTG -MN908947.3 8363 8385 SARS-CoV-2_8_RIGHT 2 - TGACTTTTTGCTACCTGCGCAT -MN908947.3 8253 8282 SARS-CoV-2_9_LEFT 1 + AGAAGTTACTGGCGATAGTTGTAATAACT -MN908947.3 9378 9400 SARS-CoV-2_9_RIGHT 1 - TGCTGATATGTCCAAAGCACCA -MN908947.3 9303 9327 SARS-CoV-2_10_LEFT 2 + TTTACCAGGAGTTTTCTGTGGTGT -MN908947.3 10429 10451 SARS-CoV-2_10_RIGHT 2 - TGGGCCTCATAGCACATTGGTA -MN908947.3 10343 10370 SARS-CoV-2_11_LEFT 1 + AGACACCTAAGTATAAGTTTGTTCGCA -MN908947.3 11447 11469 SARS-CoV-2_11_RIGHT 1 - GCCCACATGGAAATGGCTTGAT -MN908947.3 11372 11394 SARS-CoV-2_12_LEFT 2 + ATGGTGCTAGGAGAGTGTGGAC -MN908947.3 12538 12560 SARS-CoV-2_12_RIGHT 2 - GGATTTCCCACAATGCTGATGC -MN908947.3 12450 12473 SARS-CoV-2_13_LEFT 1 + ACCTCTTACAACAGCAGCCAAAC -MN908947.3 13599 13621 SARS-CoV-2_13_RIGHT 1 - CGTCCTTTTCTTGGAAGCGACA -MN908947.3 13509 13532 SARS-CoV-2_14_LEFT 2 + ACAGGCACTAGTACTGATGTCGT -MN908947.3 14619 14641 SARS-CoV-2_14_RIGHT 2 - GTGCAGCTACTGAAAAGCACGT -MN908947.3 14540 14568 SARS-CoV-2_15_LEFT 1 + TTTTAAGGAATTACTTGTGTATGCTGCT -MN908947.3 15713 15735 SARS-CoV-2_15_RIGHT 1 - ACACACAACAGCATCGTCAGAG -MN908947.3 15608 15634 SARS-CoV-2_16_LEFT 2 + ACAACACAGACTTTATGAGTGTCTCT -MN908947.3 16698 16720 SARS-CoV-2_16_RIGHT 2 - CTCTGTCAGACAGCACTTCACG -MN908947.3 16624 16647 SARS-CoV-2_17_LEFT 1 + TCAAGCTTTTTGCAGCAGAAACG -MN908947.3 17732 17754 SARS-CoV-2_17_RIGHT 1 - CCAAGCAGGGTTACGTGTAAGG -MN908947.3 17622 17649 SARS-CoV-2_18_LEFT 2 + GCACATAAAGACAAATCAGCTCAATGC -MN908947.3 18684 18706 SARS-CoV-2_18_RIGHT 2 - TGTCTGAAGCAGTGGAAAAGCA -MN908947.3 18596 18618 SARS-CoV-2_19_LEFT 1 + GGCACATGGCTTTGAGTTGACA -MN908947.3 19655 19678 SARS-CoV-2_19_RIGHT 1 - CCTGTTGTCCATCAAAGTGTCCC -MN908947.3 19574 19604 SARS-CoV-2_20_LEFT 2 + ACAATTTGATACTTATAACCTCTGGAACAC -MN908947.3 20676 20698 SARS-CoV-2_20_RIGHT 2 - GATTAGGCATAGCAACACCCGG -MN908947.3 20553 20581 SARS-CoV-2_21_LEFT 1 + TCTGTAGTTTCTAAGGTTGTCAAAGTGA -MN908947.3 21620 21642 SARS-CoV-2_21_RIGHT 1 - GCAGGGGGTAATTGAGTTCTGG -MN908947.3 21532 21562 SARS-CoV-2_22_LEFT 2 + GTGATGTTCTTGTTAACAACTAAACGAACA -MN908947.3 22590 22612 SARS-CoV-2_22_RIGHT 2 - AACAGATGCAAATCTGGTGGCG -MN908947.3 22511 22537 SARS-CoV-2_23_LEFT 1 + ACTTTAGAGTCCAACCAACAGAATCT -MN908947.3 23609 23631 SARS-CoV-2_23_RIGHT 1 - TGACTAGCTACACTACGTGCCC -MN908947.3 23518 23544 SARS-CoV-2_24_LEFT 2 + GCTGAACATGTCAACAACTCATATGA -MN908947.3 24714 24736 SARS-CoV-2_24_RIGHT 2 - ATGAGGTGCTGACTGAGGGAAG -MN908947.3 24633 24658 SARS-CoV-2_25_LEFT 1 + TGCTGCTACTAAAATGTCAGAGTGT -MN908947.3 25768 25790 SARS-CoV-2_25_RIGHT 1 - CATTTCCAGCAAAGCCAAAGCC -MN908947.3 25690 25712 SARS-CoV-2_26_LEFT 2 + GCCTTGAAGCCCCTTTTCTCTA -MN908947.3 26835 26857 SARS-CoV-2_26_RIGHT 2 - AATGACCACATGGAACGCGTAC -MN908947.3 26744 26766 SARS-CoV-2_27_LEFT 1 + TGGATCACCGGTGGAATTGCTA -MN908947.3 27872 27894 SARS-CoV-2_27_RIGHT 1 - TGTTCGTTTAGGCGTGACAAGT -MN908947.3 27784 27808 SARS-CoV-2_28_LEFT 2 + TTTGTGCTTTTTAGCCTTTCTGCT -MN908947.3 27784 27808 SARS-CoV-2_28_LEFT_27837T 2 + TTTGTGCTTTTTAGCCTTTCTGTT -MN908947.3 28985 29007 SARS-CoV-2_28_RIGHT 2 - GTTTGGCCTTGTTGTTGTTGGC -MN908947.3 28677 28699 SARS-CoV-2_29_LEFT 1 + TGAGGGAGCCTTGAATACACCA -MN908947.3 29768 29790 SARS-CoV-2_29_RIGHT 1 - TAGGCAGCTCTCCCTAGCATTG diff --git a/test/data/primer-schemes/midnight/v2/scheme.bed b/test/data/primer-schemes/midnight/v2/scheme.bed deleted file mode 100644 index b104d66..0000000 --- a/test/data/primer-schemes/midnight/v2/scheme.bed +++ /dev/null @@ -1,59 +0,0 @@ -MN908947.3 30 54 SARS-CoV-2_1_LEFT 1 + -MN908947.3 1183 1205 SARS-CoV-2_1_RIGHT 1 - -MN908947.3 1100 1128 SARS-CoV-2_2_LEFT 2 + -MN908947.3 2244 2266 SARS-CoV-2_2_RIGHT 2 - -MN908947.3 2153 2179 SARS-CoV-2_3_LEFT 1 + -MN908947.3 3235 3257 SARS-CoV-2_3_RIGHT 1 - -MN908947.3 3144 3166 SARS-CoV-2_4_LEFT 2 + -MN908947.3 4240 4262 SARS-CoV-2_4_RIGHT 2 - -MN908947.3 4167 4189 SARS-CoV-2_5_LEFT 1 + -MN908947.3 5337 5359 SARS-CoV-2_5_RIGHT 1 - -MN908947.3 5257 5286 SARS-CoV-2_6_LEFT 2 + -MN908947.3 6358 6380 SARS-CoV-2_6_RIGHT 2 - -MN908947.3 6283 6307 SARS-CoV-2_7_LEFT 1 + -MN908947.3 7379 7401 SARS-CoV-2_7_RIGHT 1 - -MN908947.3 7298 7328 SARS-CoV-2_8_LEFT 2 + -MN908947.3 8363 8385 SARS-CoV-2_8_RIGHT 2 - -MN908947.3 8253 8282 SARS-CoV-2_9_LEFT 1 + -MN908947.3 9378 9400 SARS-CoV-2_9_RIGHT 1 - -MN908947.3 9303 9327 SARS-CoV-2_10_LEFT 2 + -MN908947.3 10429 10451 SARS-CoV-2_10_RIGHT 2 - -MN908947.3 10343 10370 SARS-CoV-2_11_LEFT 1 + -MN908947.3 11447 11469 SARS-CoV-2_11_RIGHT 1 - -MN908947.3 11372 11394 SARS-CoV-2_12_LEFT 2 + -MN908947.3 12538 12560 SARS-CoV-2_12_RIGHT 2 - -MN908947.3 12450 12473 SARS-CoV-2_13_LEFT 1 + -MN908947.3 13599 13621 SARS-CoV-2_13_RIGHT 1 - -MN908947.3 13509 13532 SARS-CoV-2_14_LEFT 2 + -MN908947.3 14619 14641 SARS-CoV-2_14_RIGHT 2 - -MN908947.3 14540 14568 SARS-CoV-2_15_LEFT 1 + -MN908947.3 15713 15735 SARS-CoV-2_15_RIGHT 1 - -MN908947.3 15608 15634 SARS-CoV-2_16_LEFT 2 + -MN908947.3 16698 16720 SARS-CoV-2_16_RIGHT 2 - -MN908947.3 16624 16647 SARS-CoV-2_17_LEFT 1 + -MN908947.3 17732 17754 SARS-CoV-2_17_RIGHT 1 - -MN908947.3 17622 17649 SARS-CoV-2_18_LEFT 2 + -MN908947.3 18684 18706 SARS-CoV-2_18_RIGHT 2 - -MN908947.3 18596 18618 SARS-CoV-2_19_LEFT 1 + -MN908947.3 19655 19678 SARS-CoV-2_19_RIGHT 1 - -MN908947.3 19574 19604 SARS-CoV-2_20_LEFT 2 + -MN908947.3 20676 20698 SARS-CoV-2_20_RIGHT 2 - -MN908947.3 20553 20581 SARS-CoV-2_21_LEFT 1 + -MN908947.3 21620 21642 SARS-CoV-2_21_RIGHT 1 - -MN908947.3 21532 21562 SARS-CoV-2_22_LEFT 2 + -MN908947.3 22590 22612 SARS-CoV-2_22_RIGHT 2 - -MN908947.3 22511 22537 SARS-CoV-2_23_LEFT 1 + -MN908947.3 23609 23631 SARS-CoV-2_23_RIGHT 1 - -MN908947.3 23518 23544 SARS-CoV-2_24_LEFT 2 + -MN908947.3 24714 24736 SARS-CoV-2_24_RIGHT 2 - -MN908947.3 24633 24658 SARS-CoV-2_25_LEFT 1 + -MN908947.3 25768 25790 SARS-CoV-2_25_RIGHT 1 - -MN908947.3 25690 25712 SARS-CoV-2_26_LEFT 2 + -MN908947.3 26835 26857 SARS-CoV-2_26_RIGHT 2 - -MN908947.3 26744 26766 SARS-CoV-2_27_LEFT 1 + -MN908947.3 27872 27894 SARS-CoV-2_27_RIGHT 1 - -MN908947.3 27784 27808 SARS-CoV-2_28_LEFT 2 + -MN908947.3 27784 27808 SARS-CoV-2_28_LEFT_27837T 2 + -MN908947.3 28985 29007 SARS-CoV-2_28_RIGHT 2 - -MN908947.3 28677 28699 SARS-CoV-2_29_LEFT 1 + -MN908947.3 29768 29790 SARS-CoV-2_29_RIGHT 1 - diff --git a/test/data/primer-schemes/schemes/sars-cov-2/artic/400/v4.1.0/info.yml b/test/data/primer-schemes/schemes/sars-cov-2/artic/400/v4.1.0/info.yml new file mode 100644 index 0000000..f7b23f4 --- /dev/null +++ b/test/data/primer-schemes/schemes/sars-cov-2/artic/400/v4.1.0/info.yml @@ -0,0 +1,22 @@ +schema_version: 1.0.0a +organism: sars-cov-2 +name: artic +amplicon_size: 400 +version: v4.1.0 +derived_from: sars-cov-2/artic/400/v4.0.0 +aliases: +- ARTIC/V4.1 +developers: +- ARTIC network +vendors: +- organisation_name: IDT + kit_name: '10011442' +- organisation_name: Eurofins + home_page: https://eurofinsgenomics.com +definition_url: https://github.com/pha4ge/primer-schemes/tree/main/sars-cov-2/artic/v4.1 +source_url: https://github.com/quick-lab/primerschemes/tree/main/primerschemes/artic-sars-cov-2/400/v4.1.0 +citations: +- https://doi.org/10.1101%2F2020.09.04.283077 +license: CC-BY-SA-4.0 +primer_checksum: primaschema:3ef3e7bb23008684 +reference_checksum: primaschema:b1acd7163146bf17 diff --git a/test/data/primer-schemes/schemes/sars-cov-2/artic/400/v4.1.0/primer.bed b/test/data/primer-schemes/schemes/sars-cov-2/artic/400/v4.1.0/primer.bed new file mode 100644 index 0000000..24f0442 --- /dev/null +++ b/test/data/primer-schemes/schemes/sars-cov-2/artic/400/v4.1.0/primer.bed @@ -0,0 +1,209 @@ +MN908947.3 25 50 SARS-CoV-2_1_LEFT_1 1 + AACAAACCAACCAACTTTCGATCTC +MN908947.3 408 431 SARS-CoV-2_1_RIGHT_1 1 - CTTCTACTAAGCCACAAGTGCCA +MN908947.3 324 344 SARS-CoV-2_2_LEFT_1 2 + TTTACAGGTTCGCGACGTGC +MN908947.3 705 727 SARS-CoV-2_2_RIGHT_1 2 - ATAAGGATCAGTGCCAAGCTCG +MN908947.3 644 666 SARS-CoV-2_3_LEFT_1 1 + GTAATAAAGGAGCTGGTGGCCA +MN908947.3 1017 1044 SARS-CoV-2_3_RIGHT_1 1 - GCCAATTTAATTTCAAAAGGTGTCTGC +MN908947.3 944 966 SARS-CoV-2_4_LEFT_1 2 + GTGTATACTGCTGCCGTGAACA +MN908947.3 1337 1362 SARS-CoV-2_4_RIGHT_1 2 - ACAACAGCATTTTGGGGTAAGTAAC +MN908947.3 1245 1266 SARS-CoV-2_5_LEFT_1 1 + TGAAACTTCATGGCAGACGGG +MN908947.3 1623 1650 SARS-CoV-2_5_RIGHT_1 1 - TTGATGTTGACTTTCTCTTTTTGGAGT +MN908947.3 1540 1562 SARS-CoV-2_6_LEFT_1 2 + CGTGCTAGCGCTAACATAGGTT +MN908947.3 1925 1948 SARS-CoV-2_6_RIGHT_1 2 - AACACGCACAGAATTTTGAGCAG +MN908947.3 1851 1875 SARS-CoV-2_7_LEFT_1 1 + ACTGAGTCCTCTTTATGCATTTGC +MN908947.3 2228 2250 SARS-CoV-2_7_RIGHT_1 1 - CCACCGACAATTTCACAAGCAC +MN908947.3 2154 2180 SARS-CoV-2_8_LEFT_1 2 + GCTTGAAGAGAAGTTTAAGGAAGGTG +MN908947.3 2544 2571 SARS-CoV-2_8_RIGHT_1 2 - GGTTGTTCTAATGGTTGTAAATCACCA +MN908947.3 2483 2508 SARS-CoV-2_9_LEFT_1 1 + TCTTCTTAGAGGGAGAAACACTTCC +MN908947.3 2861 2885 SARS-CoV-2_9_RIGHT_1 1 - CACAGGCGAACTCATTTACTTCTG +MN908947.3 2780 2813 SARS-CoV-2_10_LEFT_1 2 + TGAATATCACTTTTGAACTTGATGAAAGGATTG +MN908947.3 2826 2850 SARS-CoV-2_10_LEFT_2 2 + TGAGAAGTGCTCTGCCTATACAGT +MN908947.3 3156 3177 SARS-CoV-2_10_RIGHT_1 2 - GGTTGAAGAGCAGCAGAAGTG +MN908947.3 3183 3210 SARS-CoV-2_10_RIGHT_2 2 - TCATCTAACCAATCTTCTTCTTGCTCT +MN908947.3 3078 3102 SARS-CoV-2_11_LEFT_1 1 + AGAAGAGTTTGAGCCATCAACTCA +MN908947.3 3470 3492 SARS-CoV-2_11_RIGHT_1 1 - TTTAAGGCTCCTGCAACACCTC +MN908947.3 3390 3412 SARS-CoV-2_12_LEFT_1 2 + TGCAGACATTGTGGAAGAAGCT +MN908947.3 3769 3794 SARS-CoV-2_12_RIGHT_1 2 - CAGCTAAGTAGACATTTGTGCGAAC +MN908947.3 3683 3705 SARS-CoV-2_13_LEFT_1 1 + AGCACGAAGTTCTACTTGCACC +MN908947.3 4067 4093 SARS-CoV-2_13_RIGHT_1 1 - GATGTCAATGTCACTAACAAGAGTGG +MN908947.3 3992 4018 SARS-CoV-2_14_LEFT_1 2 + TGGAAGAAACTAAGTTCCTCACAGAA +MN908947.3 4387 4409 SARS-CoV-2_14_RIGHT_1 2 - CATGTGCAAGCATTTCTCGCAA +MN908947.3 4312 4339 SARS-CoV-2_15_LEFT_1 1 + AAAAGTGCCTTTTACATTCTACCATCT +MN908947.3 4685 4710 SARS-CoV-2_15_RIGHT_1 1 - GCATCAGGTGAAGAAACAGAAACTG +MN908947.3 4620 4648 SARS-CoV-2_16_LEFT_1 2 + TGTAACACATGGCTTAAATTTGGAAGAA +MN908947.3 4995 5017 SARS-CoV-2_16_RIGHT_1 2 - CACAACTTGCGTGTGGAGGTTA +MN908947.3 4923 4953 SARS-CoV-2_17_LEFT_1 1 + TGACAATCTTAAGACACTTCTTTCTTTGAG +MN908947.3 5302 5331 SARS-CoV-2_17_RIGHT_1 1 - TTCAACTCTATTTGTTGGAGTGTTAACAA +MN908947.3 5230 5259 SARS-CoV-2_18_LEFT_1 2 + TGGAAATACCCACAAGTTAATGGTTTAAC +MN908947.3 5620 5643 SARS-CoV-2_18_RIGHT_1 2 - GCTTGTTTACCACACGTACAAGG +MN908947.3 5561 5584 SARS-CoV-2_19_LEFT_1 1 + AAGCTGTTATGTACATGGGCACA +MN908947.3 5932 5957 SARS-CoV-2_19_RIGHT_1 1 - TGTCCAACTTAGGGTCAATTTCTGT +MN908947.3 5867 5894 SARS-CoV-2_20_LEFT_1 2 + ACAAAGAAAACAGTTACACAACAACCA +MN908947.3 6247 6272 SARS-CoV-2_20_RIGHT_1 2 - ACGTGGCTTTATTAGTTGCATTGTT +MN908947.3 6184 6210 SARS-CoV-2_21_LEFT_1 1 + CACTACACACCCTCTTTTAAGAAAGG +MN908947.3 6553 6582 SARS-CoV-2_21_RIGHT_1 1 - GTAAGACTAGAATTGTCTACATAAGCAGC +MN908947.3 6478 6507 SARS-CoV-2_22_LEFT_1 2 + GTAGGAGACATTATACTTAAACCAGCAAA +MN908947.3 6859 6885 SARS-CoV-2_22_RIGHT_1 2 - CCGACACTCTTAACAGTATTCTTTGC +MN908947.3 6747 6776 SARS-CoV-2_23_LEFT_1 1 + AAACCGTGTTTGTACTAATTATATGCCTT +MN908947.3 7122 7148 SARS-CoV-2_23_RIGHT_1 1 - AACCACTAAGACAAACACTACAAGGT +MN908947.3 7127 7156 SARS-CoV-2_23_RIGHT_2 1 - AGAATCTAAACCACTAAGACAAACACTAC +MN908947.3 7057 7084 SARS-CoV-2_24_LEFT_1 2 + GGTTACAGAGAAGGCTATTTGAACTCT +MN908947.3 7440 7467 SARS-CoV-2_24_RIGHT_1 2 - ACAACATGCACATAACTTTTCCATACA +MN908947.3 7381 7403 SARS-CoV-2_25_LEFT_1 1 + CAAATGGCCCCGATTTCAGCTA +MN908947.3 7747 7770 SARS-CoV-2_25_RIGHT_1 1 - TGGATGGAACCATTCTTCACTGT +MN908947.3 7672 7695 SARS-CoV-2_26_LEFT_1 2 + GCGAGAGACTTGTCACTACAGTT +MN908947.3 8063 8092 SARS-CoV-2_26_RIGHT_1 2 - GAGTTTTTCCATTGGTACGTTAAAAGTTG +MN908947.3 7997 8019 SARS-CoV-2_27_LEFT_1 1 + CTGATGTTGGTGATAGTGCGGA +MN908947.3 8367 8392 SARS-CoV-2_27_RIGHT_1 1 - AATGTTGTGACTTTTTGCTACCTGC +MN908947.3 8370 8395 SARS-CoV-2_27_RIGHT_2 1 - AGCAATGTTGTGACTTTTTGCTACC +MN908947.3 8304 8326 SARS-CoV-2_28_LEFT_1 2 + TGAAAACATGACACCCCGTGAC +MN908947.3 8691 8714 SARS-CoV-2_28_RIGHT_1 2 - TGACACCACCATCAATAGCCTTG +MN908947.3 8596 8619 SARS-CoV-2_29_LEFT_1 1 + CTTGTGTTCCTTTTTGTTGCTGC +MN908947.3 8990 9013 SARS-CoV-2_29_RIGHT_1 1 - AGCCAAAACACAAGCTGATGTTG +MN908947.3 8919 8944 SARS-CoV-2_30_LEFT_1 2 + ACCTAGAGTTTTTAGTGCAGTTGGT +MN908947.3 9306 9329 SARS-CoV-2_30_RIGHT_1 2 - CTACACCACAGAAAACTCCTGGT +MN908947.3 9168 9192 SARS-CoV-2_31_LEFT_1 1 + CCTTGAAGGTTCTGTTAGAGTGGT +MN908947.3 9535 9564 SARS-CoV-2_31_RIGHT_1 1 - AATGAGTAAACTGGTGTTAAACAGAGTAC +MN908947.3 9470 9497 SARS-CoV-2_32_LEFT_1 2 + GAGCTTTTGGTGAATACAGTCATGTAG +MN908947.3 9842 9866 SARS-CoV-2_32_RIGHT_1 2 - GAGGTAATAGCACATCACTACGCA +MN908947.3 9782 9805 SARS-CoV-2_33_LEFT_1 1 + GTACTTTTGAAGAAGCTGCGCTG +MN908947.3 10150 10176 SARS-CoV-2_33_RIGHT_1 1 - TGTCTTGGACAGTAAACTACGTCATC +MN908947.3 10076 10099 SARS-CoV-2_34_LEFT_1 2 + TCCCATCTGGTAAAGTTGAGGGT +MN908947.3 10465 10491 SARS-CoV-2_34_RIGHT_1 2 - CCACATGAACCATTAAGGAATGAACC +MN908947.3 10393 10419 SARS-CoV-2_35_LEFT_1 1 + GTGTTAGCTTGTTACAATGGTTCACC +MN908947.3 10785 10810 SARS-CoV-2_35_RIGHT_1 1 - AGGTCCTAGTATGTCAACATGGTCT +MN908947.3 10713 10742 SARS-CoV-2_36_LEFT_1 2 + CAATCGATTTACCACAACTCTTAATGACT +MN908947.3 11092 11116 SARS-CoV-2_36_RIGHT_1 2 - ACCCATAGCAAAAGGTAAAAAGGC +MN908947.3 11000 11023 SARS-CoV-2_37_LEFT_1 1 + CACACCACTGGTTGTTACTCACA +MN908947.3 11388 11414 SARS-CoV-2_37_RIGHT_1 1 - GTGTCAAGACATTCATAAGTGTCCAC +MN908947.3 11305 11330 SARS-CoV-2_38_LEFT_1 2 + GACTGTGTTATGTATGCATCAGCTG +MN908947.3 11689 11720 SARS-CoV-2_38_RIGHT_1 2 - CCTGTGTAGAAACTAAGTAATCATAAACACC +MN908947.3 11624 11651 SARS-CoV-2_39_LEFT_1 1 + GCTATTTTTGTACTTGTTACTTTGGCC +MN908947.3 12011 12033 SARS-CoV-2_39_RIGHT_1 1 - CCCTGCATGGAAAGCAAAACAG +MN908947.3 11937 11963 SARS-CoV-2_40_LEFT_1 2 + TGTCCAGTTACACAATGACATTCTCT +MN908947.3 12317 12339 SARS-CoV-2_40_RIGHT_1 2 - ACTTTTGCCCTCTTGTCCTCAG +MN908947.3 12234 12255 SARS-CoV-2_41_LEFT_1 1 + ATTTGACCGTGATGCAGCCAT +MN908947.3 12618 12643 SARS-CoV-2_41_RIGHT_1 1 - AAGAGGCCATGCTAAATTAGGTGAA +MN908947.3 12519 12546 SARS-CoV-2_42_LEFT_1 2 + TGGTACAACATTTACTTATGCATCAGC +MN908947.3 12895 12920 SARS-CoV-2_42_RIGHT_1 2 - TGTCTGTAACAAACCTACAAGGTGG +MN908947.3 12831 12856 SARS-CoV-2_43_LEFT_1 1 + GGATTTGAAATGGGCTAGATTCCCT +MN908947.3 13218 13240 SARS-CoV-2_43_RIGHT_1 1 - CGATGCACCACCAAAGGATTCT +MN908947.3 13124 13148 SARS-CoV-2_44_LEFT_1 2 + GGGGACAACCAATCACTAATTGTG +MN908947.3 13506 13528 SARS-CoV-2_44_RIGHT_1 2 - CATCAGTACTAGTGCCTGTGCC +MN908947.3 13463 13485 SARS-CoV-2_45_LEFT_1 1 + TAAACGGGTTTGCGGTGTAAGT +MN908947.3 13833 13859 SARS-CoV-2_45_RIGHT_1 1 - TCACAATTACCTTCATCAAAATGCCT +MN908947.3 13752 13775 SARS-CoV-2_46_LEFT_1 2 + AGAATAGACGGTGACATGGTACC +MN908947.3 14120 14144 SARS-CoV-2_46_RIGHT_1 2 - TCTACAACAGGAACTCCACTACCT +MN908947.3 14045 14075 SARS-CoV-2_47_LEFT_1 1 + TGGTGTACTGACATTAGATAATCAAGATCT +MN908947.3 14428 14457 SARS-CoV-2_47_RIGHT_1 1 - TGGAACACCATCAACAAATATTTTTCTCA +MN908947.3 14338 14362 SARS-CoV-2_48_LEFT_1 2 + ACTGTTTGGATGACAGATGCATTC +MN908947.3 14717 14743 SARS-CoV-2_48_RIGHT_1 2 - CAGAACTTCCTTCCTTAAAGAAACCC +MN908947.3 14647 14674 SARS-CoV-2_49_LEFT_1 1 + ACAATGTTGCTTTTCAAACTGTCAAAC +MN908947.3 15023 15050 SARS-CoV-2_49_RIGHT_1 1 - GGGATGACATTACGTTTTGTATATGCG +MN908947.3 14953 14983 SARS-CoV-2_50_LEFT_1 2 + CATTTAATAAATGGGGTAAGGCTAGACTTT +MN908947.3 15336 15358 SARS-CoV-2_50_RIGHT_1 2 - GAGCAAGAACAAGTGAGGCCAT +MN908947.3 15214 15237 SARS-CoV-2_51_LEFT_1 1 + GCAAATTCTATGGTGGTTGGCAC +MN908947.3 15596 15619 SARS-CoV-2_51_RIGHT_1 1 - GTCTGTGTTGTAAATTGCGGACA +MN908947.3 15535 15557 SARS-CoV-2_52_LEFT_1 2 + CTGTCACGGCCAATGTTAATGC +MN908947.3 15917 15941 SARS-CoV-2_52_RIGHT_1 2 - GGATCTGGGTAAGGAAGGTACACA +MN908947.3 15855 15881 SARS-CoV-2_53_LEFT_1 1 + ACTAAAGGACCTCATGAATTTTGCTC +MN908947.3 16239 16260 SARS-CoV-2_53_RIGHT_1 1 - GCAAAGAACACAAGCCCCAAC +MN908947.3 16112 16137 SARS-CoV-2_54_LEFT_1 2 + ACATGATGAGTTAACAGGACACATG +MN908947.3 16483 16508 SARS-CoV-2_54_RIGHT_1 2 - CCAAAAACTTGTCCATTAGCACACA +MN908947.3 16386 16408 SARS-CoV-2_55_LEFT_1 1 + AATGCTCCAGGTTGTGATGTCA +MN908947.3 16767 16796 SARS-CoV-2_55_RIGHT_1 1 - ACACGATAACCAGTAAAGACATAATTTCG +MN908947.3 16692 16714 SARS-CoV-2_56_LEFT_1 2 + ACTGTACGTGAAGTGCTGTCTG +MN908947.3 17082 17105 SARS-CoV-2_56_RIGHT_1 2 - TGACTCTTACCAGTACCAGGTGG +MN908947.3 16986 17013 SARS-CoV-2_57_LEFT_1 1 + GGCTTATACCCAACACTCAATATCTCA +MN908947.3 17381 17405 SARS-CoV-2_57_RIGHT_1 1 - CTGGCATTGACAACACTCAAATCA +MN908947.3 17323 17345 SARS-CoV-2_58_LEFT_1 2 + TGCCTGAGACGACAGCAGATAT +MN908947.3 17688 17711 SARS-CoV-2_58_RIGHT_1 2 - TGTGGCCTGTTAATTGCAGATGA +MN908947.3 17615 17642 SARS-CoV-2_59_LEFT_1 1 + GCTTAAAGCACATAAAGACAAATCAGC +MN908947.3 17997 18022 SARS-CoV-2_59_RIGHT_1 1 - TCCTACGTGGAATTTCAAGACTTGT +MN908947.3 17911 17939 SARS-CoV-2_60_LEFT_1 2 + ACAGATTTAATGTTGCTATTACCAGAGC +MN908947.3 18307 18328 SARS-CoV-2_60_RIGHT_1 2 - TAGCATGACACCCCTCGACAT +MN908947.3 18244 18267 SARS-CoV-2_61_LEFT_1 1 + ACCCTAACATGTTTATCACCCGC +MN908947.3 18624 18652 SARS-CoV-2_61_RIGHT_1 1 - GCTCAGGTCCTATTTTCACAAAATACTT +MN908947.3 18550 18578 SARS-CoV-2_62_LEFT_1 2 + GTGACACACTTAAAAATCTCTCTGACAG +MN908947.3 18936 18961 SARS-CoV-2_62_RIGHT_1 2 - CCGCATTAATCTTCAGTTCATCACC +MN908947.3 18869 18891 SARS-CoV-2_63_LEFT_1 1 + TAGGTGTCTAGCTGTCCACGAG +MN908947.3 19252 19277 SARS-CoV-2_63_RIGHT_1 1 - CCAGGCAAGTTAAGGTTAGATAGCA +MN908947.3 19183 19208 SARS-CoV-2_64_LEFT_1 2 + GCCTATTTTGGAATTGCAATGTCGA +MN908947.3 19558 19586 SARS-CoV-2_64_RIGHT_1 2 - GTATCAAATTGTTTGTAAACCCACAAGC +MN908947.3 19485 19513 SARS-CoV-2_65_LEFT_1 1 + GTCTGTAGACATCATGCTAATGAGTACA +MN908947.3 19877 19901 SARS-CoV-2_65_RIGHT_1 1 - GCTGGAGCATCTCTTTTGTAGTCC +MN908947.3 19810 19836 SARS-CoV-2_66_LEFT_1 2 + AACCAGTACCAGAGGTGAAAATACTC +MN908947.3 20186 20216 SARS-CoV-2_66_RIGHT_1 2 - TTTCTACTCTGAGTAAAGTAAGTTTCAGGT +MN908947.3 20090 20117 SARS-CoV-2_67_LEFT_1 1 + CAAACAAGCTAGTCTTAATGGAGTCAC +MN908947.3 20472 20497 SARS-CoV-2_67_RIGHT_1 1 - AACACACACACTTAGATGAACCTGT +MN908947.3 20377 20405 SARS-CoV-2_68_LEFT_1 2 + GACTAGCTAAACGTTTTAAGGAATCACC +MN908947.3 20766 20792 SARS-CoV-2_68_RIGHT_1 2 - GCGACATTCATCATTATGCCTTTAGG +MN908947.3 20677 20699 SARS-CoV-2_69_LEFT_1 1 + CGGGTGTTGCTATGCCTAATCT +MN908947.3 21050 21080 SARS-CoV-2_69_RIGHT_1 1 - TTTGTAACATTTTTAGTCTTAGGGTCGTAC +MN908947.3 20988 21013 SARS-CoV-2_70_LEFT_1 2 + TTGATTGGTGATTGTGCAACTGTAC +MN908947.3 21358 21387 SARS-CoV-2_70_RIGHT_1 2 - AGAATAGGAAGACAACTGAATTGGATTTG +MN908947.3 21294 21316 SARS-CoV-2_71_LEFT_1 1 + GGCAAACCACGCGAACAAATAG +MN908947.3 21675 21700 SARS-CoV-2_71_RIGHT_1 1 - TGAGGATCTGAAAACTTTGTCAGGG +MN908947.3 21532 21561 SARS-CoV-2_72_LEFT_1 2 + GTGATGTTCTTGTTAACAACTAAACGAAC +MN908947.3 21904 21933 SARS-CoV-2_72_RIGHT_1 2 - GTAGCGTTATTAACAATAAGTAGGGACTG +MN908947.3 21865 21889 SARS-CoV-2_73_LEFT_1 1 + AGAGGCTGGATTTTTGGTACTACT +MN908947.3 22247 22274 SARS-CoV-2_73_RIGHT_1 1 - ACCTAGTGATGTTAATACCTATTGGCA +MN908947.3 22091 22113 SARS-CoV-2_74_LEFT_1 2 + TGGACCTTGAAGGAAAACAGGG +MN908947.3 22474 22503 SARS-CoV-2_74_RIGHT_1 2 - TGATAGATTCCTTTTTCTACAGTGAAGGA +MN908947.3 22402 22428 SARS-CoV-2_75_LEFT_1 1 + GAAAATGGAACCATTACAGATGCTGT +MN908947.3 22785 22805 SARS-CoV-2_75_RIGHT_1 1 - TTTGCCCTGGAGCGATTTGT +MN908947.3 22648 22677 SARS-CoV-2_76_LEFT_2 2 + GCTGATTATTCTGTCCTATATAATTCCGC +MN908947.3 22742 22774 SARS-CoV-2_76_LEFT_1 2 + ATGTCTATGCAGATTCATTTGTAATTAGAGGT +MN908947.3 23028 23057 SARS-CoV-2_76_RIGHT_2 2 - GTTGGAAACCATATGATTGTAAAGGAAAG +MN908947.3 23120 23141 SARS-CoV-2_76_RIGHT_1 2 - GTCCACAAACAGTTGCTGGTG +MN908947.3 22944 22974 SARS-CoV-2_77_LEFT_1 1 + CAAACCTTTTGAGAGAGATATTTCAACTGA +MN908947.3 23327 23351 SARS-CoV-2_77_RIGHT_1 1 - CACTGACACCACCAAAAGAACATG +MN908947.3 23219 23246 SARS-CoV-2_78_LEFT_1 2 + CTGAGTCTAACAAAAAGTTTCTGCCTT +MN908947.3 23611 23635 SARS-CoV-2_78_RIGHT_1 2 - GGATTGACTAGCTACACTACGTGC +MN908947.3 23553 23575 SARS-CoV-2_79_LEFT_1 1 + ACCCATTGGTGCAGGTATATGC +MN908947.3 23914 23944 SARS-CoV-2_79_RIGHT_1 1 - AATTGGTGGTGTTTTGTAAATTTGTTTGAC +MN908947.3 23927 23955 SARS-CoV-2_79_RIGHT_2 1 - CCAAAATCTTTAATTGGTGGTGTTTTGT +MN908947.3 23853 23876 SARS-CoV-2_80_LEFT_1 2 + CCGTGCTTTAACTGGAATAGCTG +MN908947.3 24233 24258 SARS-CoV-2_80_RIGHT_1 2 - GCAAATGGTATTTGTAATGCAGCAC +MN908947.3 24171 24194 SARS-CoV-2_81_LEFT_1 1 + TGCTCAATACACTTCTGCACTGT +MN908947.3 24545 24567 SARS-CoV-2_81_RIGHT_1 1 - TGAAGTCTGCCTGTGATCAACC +MN908947.3 24426 24448 SARS-CoV-2_82_LEFT_1 2 + TGCACAAGCTTTAAACACGCTT +MN908947.3 24814 24836 SARS-CoV-2_82_RIGHT_1 2 - CACGAGGAAAGTGTGCTTTTCC +MN908947.3 24750 24772 SARS-CoV-2_83_LEFT_1 1 + GCATGTGACTTATGTCCCTGCA +MN908947.3 25122 25150 SARS-CoV-2_83_RIGHT_1 1 - AGATTCATTTAAATTCTTGGCAACCTCA +MN908947.3 25051 25076 SARS-CoV-2_84_LEFT_1 2 + GTTGATTTAGGTGACATCTCTGGCA +MN908947.3 25438 25461 SARS-CoV-2_84_RIGHT_1 2 - AGCATCCTTGATTTCACCTTGCT +MN908947.3 25331 25353 SARS-CoV-2_85_LEFT_1 1 + ATGAAGACGACTCTGAGCCAGT +MN908947.3 25711 25740 SARS-CoV-2_85_RIGHT_1 1 - CTGCAAGAAGTAGACTAAAGCATAAAGAT +MN908947.3 25645 25672 SARS-CoV-2_86_LEFT_1 2 + TGTTGTTTGTAACAGTTTACTCACACC +MN908947.3 26026 26050 SARS-CoV-2_86_RIGHT_1 2 - TCAATTGAGTTGAGTACAGCTGGT +MN908947.3 25951 25979 SARS-CoV-2_87_LEFT_1 1 + GTGGTTATACTGAAAAATGGGAATCTGG +MN908947.3 26338 26360 SARS-CoV-2_87_RIGHT_1 1 - AATCGAAGCGCAGTAAGGATGG +MN908947.3 26242 26268 SARS-CoV-2_88_LEFT_2 2 + TTATGTACTCATTCGTTTCGGAAGAG +MN908947.3 26255 26277 SARS-CoV-2_88_LEFT_1 2 + CGTTTCGGAAGAGACAGGTACG +MN908947.3 26635 26661 SARS-CoV-2_88_RIGHT_1 2 - ACAAAAACCTATTCCTGTTGGCATAG +MN908947.3 26564 26587 SARS-CoV-2_89_LEFT_1 1 + AAGCTCCTTGAACAATGGAACCT +MN908947.3 26592 26621 SARS-CoV-2_89_LEFT_2 1 + TAGGTTTCCTATTCCTTACATGGATTTGT +MN908947.3 26956 26979 SARS-CoV-2_89_RIGHT_1 1 - CAGCAATACGAAGATGTCCACGA +MN908947.3 26966 26991 SARS-CoV-2_89_RIGHT_2 1 - CTAGATGGTGTCCAGCAATACGAAG +MN908947.3 26873 26895 SARS-CoV-2_90_LEFT_1 2 + ATTCTTCTCAACGTGCCACTCC +MN908947.3 27218 27251 SARS-CoV-2_90_RIGHT_1 2 - ATTAGTAATATCTCTGCTATAGTAACCTGAAAG +MN908947.3 27256 27283 SARS-CoV-2_90_RIGHT_2 2 - TCCAAATGGAAACTTTAAAAGTCCTCA +MN908947.3 27152 27177 SARS-CoV-2_91_LEFT_1 1 + TCCAGTAGCAGTGACAATATTGCTT +MN908947.3 27534 27560 SARS-CoV-2_91_RIGHT_1 1 - AGTGCAAATTTGTTATCAGCTAGAGG +MN908947.3 27447 27473 SARS-CoV-2_92_LEFT_1 2 + CACTACCAAGAGTGTGTTAGAGGTAC +MN908947.3 27826 27855 SARS-CoV-2_92_RIGHT_1 2 - GTTCAAGTGAGAACCAAAAGATAATAAGC +MN908947.3 27700 27726 SARS-CoV-2_93_LEFT_1 1 + TTGTTGCGGCAATAGTGTTTATAACA +MN908947.3 28082 28104 SARS-CoV-2_93_RIGHT_1 1 - TGGGTGATTTAGAACCAGCCTC +MN908947.3 27996 28021 SARS-CoV-2_94_LEFT_1 2 + ACCCGTGTCCTATTCACTTCTATTC +MN908947.3 28394 28416 SARS-CoV-2_94_RIGHT_1 2 - TTATTGGGTAAACCTTGGGGCC +MN908947.3 28190 28214 SARS-CoV-2_95_LEFT_1 1 + GTGCGTTGTTCGTTCTATGAAGAC +MN908947.3 28572 28598 SARS-CoV-2_95_RIGHT_1 1 - ACCATCTTGGACTGAGATCTTTCATT +MN908947.3 28512 28536 SARS-CoV-2_96_LEFT_1 2 + AGATGACCAAATTGGCTACTACCG +MN908947.3 28893 28914 SARS-CoV-2_96_RIGHT_1 2 - CCATTGCCAGCCATTCTAGCA +MN908947.3 28827 28849 SARS-CoV-2_97_LEFT_1 1 + TTCCTCATCACGTAGTCGCAAC +MN908947.3 29206 29227 SARS-CoV-2_97_RIGHT_1 1 - CGACATTCCGAAGAACGCTGA +MN908947.3 29136 29161 SARS-CoV-2_98_LEFT_1 2 + CCAGGAACTAATCAGACAAGGAACT +MN908947.3 29512 29534 SARS-CoV-2_98_RIGHT_1 2 - TTTAGGCCTGAGTTGAGTCAGC +MN908947.3 29452 29475 SARS-CoV-2_99_LEFT_1 1 + CTTCTTCCTGCTGCAGATTTGGA +MN908947.3 29827 29854 SARS-CoV-2_99_RIGHT_1 1 - GCTATTAAAATCACATGGGGATAGCAC diff --git a/test/data/primer-schemes/schemes/sars-cov-2/artic/400/v4.1.0/primer.svg b/test/data/primer-schemes/schemes/sars-cov-2/artic/400/v4.1.0/primer.svg new file mode 100644 index 0000000..c6b07a4 --- /dev/null +++ b/test/data/primer-schemes/schemes/sars-cov-2/artic/400/v4.1.0/primer.svg @@ -0,0 +1 @@ +12pool02,0004,0006,0008,00010,00012,00014,00016,00018,00020,00022,00024,00026,00028,00030,000MN908947.3+-strand \ No newline at end of file diff --git a/test/data/primer-schemes/schemes/sars-cov-2/artic/400/v4.1.0/reference.fasta b/test/data/primer-schemes/schemes/sars-cov-2/artic/400/v4.1.0/reference.fasta new file mode 100644 index 0000000..e1cfd92 --- /dev/null +++ b/test/data/primer-schemes/schemes/sars-cov-2/artic/400/v4.1.0/reference.fasta @@ -0,0 +1,429 @@ +>MN908947.3 +ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAA +CGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAAC +TAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTG +TTGCAGCCGATCATCAGCACATCTAGGTTTCGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTC +CCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTAC +GTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGG +CTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAAACGTTCGGAT +GCTCGAACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACTCGAAGGCATTCAGTACGGTC +GTAGTGGTGAGACACTTGGTGTCCTTGTCCCTCATGTGGGCGAAATACCAGTGGCTTACCGCAAGGTTCT +TCTTCGTAAGAACGGTAATAAAGGAGCTGGTGGCCATAGTTACGGCGCCGATCTAAAGTCATTTGACTTA +GGCGACGAGCTTGGCACTGATCCTTATGAAGATTTTCAAGAAAACTGGAACACTAAACATAGCAGTGGTG +TTACCCGTGAACTCATGCGTGAGCTTAACGGAGGGGCATACACTCGCTATGTCGATAACAACTTCTGTGG +CCCTGATGGCTACCCTCTTGAGTGCATTAAAGACCTTCTAGCACGTGCTGGTAAAGCTTCATGCACTTTG +TCCGAACAACTGGACTTTATTGACACTAAGAGGGGTGTATACTGCTGCCGTGAACATGAGCATGAAATTG +CTTGGTACACGGAACGTTCTGAAAAGAGCTATGAATTGCAGACACCTTTTGAAATTAAATTGGCAAAGAA +ATTTGACACCTTCAATGGGGAATGTCCAAATTTTGTATTTCCCTTAAATTCCATAATCAAGACTATTCAA +CCAAGGGTTGAAAAGAAAAAGCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCCAGTTGCGTCAC +CAAATGAATGCAACCAAATGTGCCTTTCAACTCTCATGAAGTGTGATCATTGTGGTGAAACTTCATGGCA +GACGGGCGATTTTGTTAAAGCCACTTGCGAATTTTGTGGCACTGAGAATTTGACTAAAGAAGGTGCCACT +ACTTGTGGTTACTTACCCCAAAATGCTGTTGTTAAAATTTATTGTCCAGCATGTCACAATTCAGAAGTAG +GACCTGAGCATAGTCTTGCCGAATACCATAATGAATCTGGCTTGAAAACCATTCTTCGTAAGGGTGGTCG +CACTATTGCCTTTGGAGGCTGTGTGTTCTCTTATGTTGGTTGCCATAACAAGTGTGCCTATTGGGTTCCA +CGTGCTAGCGCTAACATAGGTTGTAACCATACAGGTGTTGTTGGAGAAGGTTCCGAAGGTCTTAATGACA +ACCTTCTTGAAATACTCCAAAAAGAGAAAGTCAACATCAATATTGTTGGTGACTTTAAACTTAATGAAGA +GATCGCCATTATTTTGGCATCTTTTTCTGCTTCCACAAGTGCTTTTGTGGAAACTGTGAAAGGTTTGGAT +TATAAAGCATTCAAACAAATTGTTGAATCCTGTGGTAATTTTAAAGTTACAAAAGGAAAAGCTAAAAAAG +GTGCCTGGAATATTGGTGAACAGAAATCAATACTGAGTCCTCTTTATGCATTTGCATCAGAGGCTGCTCG +TGTTGTACGATCAATTTTCTCCCGCACTCTTGAAACTGCTCAAAATTCTGTGCGTGTTTTACAGAAGGCC +GCTATAACAATACTAGATGGAATTTCACAGTATTCACTGAGACTCATTGATGCTATGATGTTCACATCTG +ATTTGGCTACTAACAATCTAGTTGTAATGGCCTACATTACAGGTGGTGTTGTTCAGTTGACTTCGCAGTG +GCTAACTAACATCTTTGGCACTGTTTATGAAAAACTCAAACCCGTCCTTGATTGGCTTGAAGAGAAGTTT +AAGGAAGGTGTAGAGTTTCTTAGAGACGGTTGGGAAATTGTTAAATTTATCTCAACCTGTGCTTGTGAAA +TTGTCGGTGGACAAATTGTCACCTGTGCAAAGGAAATTAAGGAGAGTGTTCAGACATTCTTTAAGCTTGT +AAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGCCTTGAATTTA +GGTGAAACATTTGTCACGCACTCAAAGGGATTGTACAGAAAGTGTGTTAAATCCAGAGAAGAAACTGGCC +TACTCATGCCTCTAAAAGCCCCAAAAGAAATTATCTTCTTAGAGGGAGAAACACTTCCCACAGAAGTGTT +AACAGAGGAAGTTGTCTTGAAAACTGGTGATTTACAACCATTAGAACAACCTACTAGTGAAGCTGTTGAA +GCTCCATTGGTTGGTACACCAGTTTGTATTAACGGGCTTATGTTGCTCGAAATCAAAGACACAGAAAAGT +ACTGTGCCCTTGCACCTAATATGATGGTAACAAACAATACCTTCACACTCAAAGGCGGTGCACCAACAAA +GGTTACTTTTGGTGATGACACTGTGATAGAAGTGCAAGGTTACAAGAGTGTGAATATCACTTTTGAACTT +GATGAAAGGATTGATAAAGTACTTAATGAGAAGTGCTCTGCCTATACAGTTGAACTCGGTACAGAAGTAA +ATGAGTTCGCCTGTGTTGTGGCAGATGCTGTCATAAAAACTTTGCAACCAGTATCTGAATTACTTACACC +ACTGGGCATTGATTTAGATGAGTGGAGTATGGCTACATACTACTTATTTGATGAGTCTGGTGAGTTTAAA +TTGGCTTCACATATGTATTGTTCTTTCTACCCTCCAGATGAGGATGAAGAAGAAGGTGATTGTGAAGAAG +AAGAGTTTGAGCCATCAACTCAATATGAGTATGGTACTGAAGATGATTACCAAGGTAAACCTTTGGAATT +TGGTGCCACTTCTGCTGCTCTTCAACCTGAAGAAGAGCAAGAAGAAGATTGGTTAGATGATGATAGTCAA +CAAACTGTTGGTCAACAAGACGGCAGTGAGGACAATCAGACAACTACTATTCAAACAATTGTTGAGGTTC +AACCTCAATTAGAGATGGAACTTACACCAGTTGTTCAGACTATTGAAGTGAATAGTTTTAGTGGTTATTT +AAAACTTACTGACAATGTATACATTAAAAATGCAGACATTGTGGAAGAAGCTAAAAAGGTAAAACCAACA +GTGGTTGTTAATGCAGCCAATGTTTACCTTAAACATGGAGGAGGTGTTGCAGGAGCCTTAAATAAGGCTA +CTAACAATGCCATGCAAGTTGAATCTGATGATTACATAGCTACTAATGGACCACTTAAAGTGGGTGGTAG +TTGTGTTTTAAGCGGACACAATCTTGCTAAACACTGTCTTCATGTTGTCGGCCCAAATGTTAACAAAGGT +GAAGACATTCAACTTCTTAAGAGTGCTTATGAAAATTTTAATCAGCACGAAGTTCTACTTGCACCATTAT +TATCAGCTGGTATTTTTGGTGCTGACCCTATACATTCTTTAAGAGTTTGTGTAGATACTGTTCGCACAAA +TGTCTACTTAGCTGTCTTTGATAAAAATCTCTATGACAAACTTGTTTCAAGCTTTTTGGAAATGAAGAGT +GAAAAGCAAGTTGAACAAAAGATCGCTGAGATTCCTAAAGAGGAAGTTAAGCCATTTATAACTGAAAGTA +AACCTTCAGTTGAACAGAGAAAACAAGATGATAAGAAAATCAAAGCTTGTGTTGAAGAAGTTACAACAAC +TCTGGAAGAAACTAAGTTCCTCACAGAAAACTTGTTACTTTATATTGACATTAATGGCAATCTTCATCCA +GATTCTGCCACTCTTGTTAGTGACATTGACATCACTTTCTTAAAGAAAGATGCTCCATATATAGTGGGTG +ATGTTGTTCAAGAGGGTGTTTTAACTGCTGTGGTTATACCTACTAAAAAGGCTGGTGGCACTACTGAAAT +GCTAGCGAAAGCTTTGAGAAAAGTGCCAACAGACAATTATATAACCACTTACCCGGGTCAGGGTTTAAAT +GGTTACACTGTAGAGGAGGCAAAGACAGTGCTTAAAAAGTGTAAAAGTGCCTTTTACATTCTACCATCTA +TTATCTCTAATGAGAAGCAAGAAATTCTTGGAACTGTTTCTTGGAATTTGCGAGAAATGCTTGCACATGC +AGAAGAAACACGCAAATTAATGCCTGTCTGTGTGGAAACTAAAGCCATAGTTTCAACTATACAGCGTAAA +TATAAGGGTATTAAAATACAAGAGGGTGTGGTTGATTATGGTGCTAGATTTTACTTTTACACCAGTAAAA +CAACTGTAGCGTCACTTATCAACACACTTAACGATCTAAATGAAACTCTTGTTACAATGCCACTTGGCTA +TGTAACACATGGCTTAAATTTGGAAGAAGCTGCTCGGTATATGAGATCTCTCAAAGTGCCAGCTACAGTT +TCTGTTTCTTCACCTGATGCTGTTACAGCGTATAATGGTTATCTTACTTCTTCTTCTAAAACACCTGAAG +AACATTTTATTGAAACCATCTCACTTGCTGGTTCCTATAAAGATTGGTCCTATTCTGGACAATCTACACA +ACTAGGTATAGAATTTCTTAAGAGAGGTGATAAAAGTGTATATTACACTAGTAATCCTACCACATTCCAC +CTAGATGGTGAAGTTATCACCTTTGACAATCTTAAGACACTTCTTTCTTTGAGAGAAGTGAGGACTATTA +AGGTGTTTACAACAGTAGACAACATTAACCTCCACACGCAAGTTGTGGACATGTCAATGACATATGGACA +ACAGTTTGGTCCAACTTATTTGGATGGAGCTGATGTTACTAAAATAAAACCTCATAATTCACATGAAGGT +AAAACATTTTATGTTTTACCTAATGATGACACTCTACGTGTTGAGGCTTTTGAGTACTACCACACAACTG +ATCCTAGTTTTCTGGGTAGGTACATGTCAGCATTAAATCACACTAAAAAGTGGAAATACCCACAAGTTAA +TGGTTTAACTTCTATTAAATGGGCAGATAACAACTGTTATCTTGCCACTGCATTGTTAACACTCCAACAA +ATAGAGTTGAAGTTTAATCCACCTGCTCTACAAGATGCTTATTACAGAGCAAGGGCTGGTGAAGCTGCTA +ACTTTTGTGCACTTATCTTAGCCTACTGTAATAAGACAGTAGGTGAGTTAGGTGATGTTAGAGAAACAAT +GAGTTACTTGTTTCAACATGCCAATTTAGATTCTTGCAAAAGAGTCTTGAACGTGGTGTGTAAAACTTGT +GGACAACAGCAGACAACCCTTAAGGGTGTAGAAGCTGTTATGTACATGGGCACACTTTCTTATGAACAAT +TTAAGAAAGGTGTTCAGATACCTTGTACGTGTGGTAAACAAGCTACAAAATATCTAGTACAACAGGAGTC +ACCTTTTGTTATGATGTCAGCACCACCTGCTCAGTATGAACTTAAGCATGGTACATTTACTTGTGCTAGT +GAGTACACTGGTAATTACCAGTGTGGTCACTATAAACATATAACTTCTAAAGAAACTTTGTATTGCATAG +ACGGTGCTTTACTTACAAAGTCCTCAGAATACAAAGGTCCTATTACGGATGTTTTCTACAAAGAAAACAG +TTACACAACAACCATAAAACCAGTTACTTATAAATTGGATGGTGTTGTTTGTACAGAAATTGACCCTAAG +TTGGACAATTATTATAAGAAAGACAATTCTTATTTCACAGAGCAACCAATTGATCTTGTACCAAACCAAC +CATATCCAAACGCAAGCTTCGATAATTTTAAGTTTGTATGTGATAATATCAAATTTGCTGATGATTTAAA +CCAGTTAACTGGTTATAAGAAACCTGCTTCAAGAGAGCTTAAAGTTACATTTTTCCCTGACTTAAATGGT +GATGTGGTGGCTATTGATTATAAACACTACACACCCTCTTTTAAGAAAGGAGCTAAATTGTTACATAAAC +CTATTGTTTGGCATGTTAACAATGCAACTAATAAAGCCACGTATAAACCAAATACCTGGTGTATACGTTG +TCTTTGGAGCACAAAACCAGTTGAAACATCAAATTCGTTTGATGTACTGAAGTCAGAGGACGCGCAGGGA +ATGGATAATCTTGCCTGCGAAGATCTAAAACCAGTCTCTGAAGAAGTAGTGGAAAATCCTACCATACAGA +AAGACGTTCTTGAGTGTAATGTGAAAACTACCGAAGTTGTAGGAGACATTATACTTAAACCAGCAAATAA +TAGTTTAAAAATTACAGAAGAGGTTGGCCACACAGATCTAATGGCTGCTTATGTAGACAATTCTAGTCTT +ACTATTAAGAAACCTAATGAATTATCTAGAGTATTAGGTTTGAAAACCCTTGCTACTCATGGTTTAGCTG +CTGTTAATAGTGTCCCTTGGGATACTATAGCTAATTATGCTAAGCCTTTTCTTAACAAAGTTGTTAGTAC +AACTACTAACATAGTTACACGGTGTTTAAACCGTGTTTGTACTAATTATATGCCTTATTTCTTTACTTTA +TTGCTACAATTGTGTACTTTTACTAGAAGTACAAATTCTAGAATTAAAGCATCTATGCCGACTACTATAG +CAAAGAATACTGTTAAGAGTGTCGGTAAATTTTGTCTAGAGGCTTCATTTAATTATTTGAAGTCACCTAA +TTTTTCTAAACTGATAAATATTATAATTTGGTTTTTACTATTAAGTGTTTGCCTAGGTTCTTTAATCTAC +TCAACCGCTGCTTTAGGTGTTTTAATGTCTAATTTAGGCATGCCTTCTTACTGTACTGGTTACAGAGAAG +GCTATTTGAACTCTACTAATGTCACTATTGCAACCTACTGTACTGGTTCTATACCTTGTAGTGTTTGTCT +TAGTGGTTTAGATTCTTTAGACACCTATCCTTCTTTAGAAACTATACAAATTACCATTTCATCTTTTAAA +TGGGATTTAACTGCTTTTGGCTTAGTTGCAGAGTGGTTTTTGGCATATATTCTTTTCACTAGGTTTTTCT +ATGTACTTGGATTGGCTGCAATCATGCAATTGTTTTTCAGCTATTTTGCAGTACATTTTATTAGTAATTC +TTGGCTTATGTGGTTAATAATTAATCTTGTACAAATGGCCCCGATTTCAGCTATGGTTAGAATGTACATC +TTCTTTGCATCATTTTATTATGTATGGAAAAGTTATGTGCATGTTGTAGACGGTTGTAATTCATCAACTT +GTATGATGTGTTACAAACGTAATAGAGCAACAAGAGTCGAATGTACAACTATTGTTAATGGTGTTAGAAG +GTCCTTTTATGTCTATGCTAATGGAGGTAAAGGCTTTTGCAAACTACACAATTGGAATTGTGTTAATTGT +GATACATTCTGTGCTGGTAGTACATTTATTAGTGATGAAGTTGCGAGAGACTTGTCACTACAGTTTAAAA +GACCAATAAATCCTACTGACCAGTCTTCTTACATCGTTGATAGTGTTACAGTGAAGAATGGTTCCATCCA +TCTTTACTTTGATAAAGCTGGTCAAAAGACTTATGAAAGACATTCTCTCTCTCATTTTGTTAACTTAGAC +AACCTGAGAGCTAATAACACTAAAGGTTCATTGCCTATTAATGTTATAGTTTTTGATGGTAAATCAAAAT +GTGAAGAATCATCTGCAAAATCAGCGTCTGTTTACTACAGTCAGCTTATGTGTCAACCTATACTGTTACT +AGATCAGGCATTAGTGTCTGATGTTGGTGATAGTGCGGAAGTTGCAGTTAAAATGTTTGATGCTTACGTT +AATACGTTTTCATCAACTTTTAACGTACCAATGGAAAAACTCAAAACACTAGTTGCAACTGCAGAAGCTG +AACTTGCAAAGAATGTGTCCTTAGACAATGTCTTATCTACTTTTATTTCAGCAGCTCGGCAAGGGTTTGT +TGATTCAGATGTAGAAACTAAAGATGTTGTTGAATGTCTTAAATTGTCACATCAATCTGACATAGAAGTT +ACTGGCGATAGTTGTAATAACTATATGCTCACCTATAACAAAGTTGAAAACATGACACCCCGTGACCTTG +GTGCTTGTATTGACTGTAGTGCGCGTCATATTAATGCGCAGGTAGCAAAAAGTCACAACATTGCTTTGAT +ATGGAACGTTAAAGATTTCATGTCATTGTCTGAACAACTACGAAAACAAATACGTAGTGCTGCTAAAAAG +AATAACTTACCTTTTAAGTTGACATGTGCAACTACTAGACAAGTTGTTAATGTTGTAACAACAAAGATAG +CACTTAAGGGTGGTAAAATTGTTAATAATTGGTTGAAGCAGTTAATTAAAGTTACACTTGTGTTCCTTTT +TGTTGCTGCTATTTTCTATTTAATAACACCTGTTCATGTCATGTCTAAACATACTGACTTTTCAAGTGAA +ATCATAGGATACAAGGCTATTGATGGTGGTGTCACTCGTGACATAGCATCTACAGATACTTGTTTTGCTA +ACAAACATGCTGATTTTGACACATGGTTTAGCCAGCGTGGTGGTAGTTATACTAATGACAAAGCTTGCCC +ATTGATTGCTGCAGTCATAACAAGAGAAGTGGGTTTTGTCGTGCCTGGTTTGCCTGGCACGATATTACGC +ACAACTAATGGTGACTTTTTGCATTTCTTACCTAGAGTTTTTAGTGCAGTTGGTAACATCTGTTACACAC +CATCAAAACTTATAGAGTACACTGACTTTGCAACATCAGCTTGTGTTTTGGCTGCTGAATGTACAATTTT +TAAAGATGCTTCTGGTAAGCCAGTACCATATTGTTATGATACCAATGTACTAGAAGGTTCTGTTGCTTAT +GAAAGTTTACGCCCTGACACACGTTATGTGCTCATGGATGGCTCTATTATTCAATTTCCTAACACCTACC +TTGAAGGTTCTGTTAGAGTGGTAACAACTTTTGATTCTGAGTACTGTAGGCACGGCACTTGTGAAAGATC +AGAAGCTGGTGTTTGTGTATCTACTAGTGGTAGATGGGTACTTAACAATGATTATTACAGATCTTTACCA +GGAGTTTTCTGTGGTGTAGATGCTGTAAATTTACTTACTAATATGTTTACACCACTAATTCAACCTATTG +GTGCTTTGGACATATCAGCATCTATAGTAGCTGGTGGTATTGTAGCTATCGTAGTAACATGCCTTGCCTA +CTATTTTATGAGGTTTAGAAGAGCTTTTGGTGAATACAGTCATGTAGTTGCCTTTAATACTTTACTATTC +CTTATGTCATTCACTGTACTCTGTTTAACACCAGTTTACTCATTCTTACCTGGTGTTTATTCTGTTATTT +ACTTGTACTTGACATTTTATCTTACTAATGATGTTTCTTTTTTAGCACATATTCAGTGGATGGTTATGTT +CACACCTTTAGTACCTTTCTGGATAACAATTGCTTATATCATTTGTATTTCCACAAAGCATTTCTATTGG +TTCTTTAGTAATTACCTAAAGAGACGTGTAGTCTTTAATGGTGTTTCCTTTAGTACTTTTGAAGAAGCTG +CGCTGTGCACCTTTTTGTTAAATAAAGAAATGTATCTAAAGTTGCGTAGTGATGTGCTATTACCTCTTAC +GCAATATAATAGATACTTAGCTCTTTATAATAAGTACAAGTATTTTAGTGGAGCAATGGATACAACTAGC +TACAGAGAAGCTGCTTGTTGTCATCTCGCAAAGGCTCTCAATGACTTCAGTAACTCAGGTTCTGATGTTC +TTTACCAACCACCACAAACCTCTATCACCTCAGCTGTTTTGCAGAGTGGTTTTAGAAAAATGGCATTCCC +ATCTGGTAAAGTTGAGGGTTGTATGGTACAAGTAACTTGTGGTACAACTACACTTAACGGTCTTTGGCTT +GATGACGTAGTTTACTGTCCAAGACATGTGATCTGCACCTCTGAAGACATGCTTAACCCTAATTATGAAG +ATTTACTCATTCGTAAGTCTAATCATAATTTCTTGGTACAGGCTGGTAATGTTCAACTCAGGGTTATTGG +ACATTCTATGCAAAATTGTGTACTTAAGCTTAAGGTTGATACAGCCAATCCTAAGACACCTAAGTATAAG +TTTGTTCGCATTCAACCAGGACAGACTTTTTCAGTGTTAGCTTGTTACAATGGTTCACCATCTGGTGTTT +ACCAATGTGCTATGAGGCCCAATTTCACTATTAAGGGTTCATTCCTTAATGGTTCATGTGGTAGTGTTGG +TTTTAACATAGATTATGACTGTGTCTCTTTTTGTTACATGCACCATATGGAATTACCAACTGGAGTTCAT +GCTGGCACAGACTTAGAAGGTAACTTTTATGGACCTTTTGTTGACAGGCAAACAGCACAAGCAGCTGGTA +CGGACACAACTATTACAGTTAATGTTTTAGCTTGGTTGTACGCTGCTGTTATAAATGGAGACAGGTGGTT +TCTCAATCGATTTACCACAACTCTTAATGACTTTAACCTTGTGGCTATGAAGTACAATTATGAACCTCTA +ACACAAGACCATGTTGACATACTAGGACCTCTTTCTGCTCAAACTGGAATTGCCGTTTTAGATATGTGTG +CTTCATTAAAAGAATTACTGCAAAATGGTATGAATGGACGTACCATATTGGGTAGTGCTTTATTAGAAGA +TGAATTTACACCTTTTGATGTTGTTAGACAATGCTCAGGTGTTACTTTCCAAAGTGCAGTGAAAAGAACA +ATCAAGGGTACACACCACTGGTTGTTACTCACAATTTTGACTTCACTTTTAGTTTTAGTCCAGAGTACTC +AATGGTCTTTGTTCTTTTTTTTGTATGAAAATGCCTTTTTACCTTTTGCTATGGGTATTATTGCTATGTC +TGCTTTTGCAATGATGTTTGTCAAACATAAGCATGCATTTCTCTGTTTGTTTTTGTTACCTTCTCTTGCC +ACTGTAGCTTATTTTAATATGGTCTATATGCCTGCTAGTTGGGTGATGCGTATTATGACATGGTTGGATA +TGGTTGATACTAGTTTGTCTGGTTTTAAGCTAAAAGACTGTGTTATGTATGCATCAGCTGTAGTGTTACT +AATCCTTATGACAGCAAGAACTGTGTATGATGATGGTGCTAGGAGAGTGTGGACACTTATGAATGTCTTG +ACACTCGTTTATAAAGTTTATTATGGTAATGCTTTAGATCAAGCCATTTCCATGTGGGCTCTTATAATCT +CTGTTACTTCTAACTACTCAGGTGTAGTTACAACTGTCATGTTTTTGGCCAGAGGTATTGTTTTTATGTG +TGTTGAGTATTGCCCTATTTTCTTCATAACTGGTAATACACTTCAGTGTATAATGCTAGTTTATTGTTTC +TTAGGCTATTTTTGTACTTGTTACTTTGGCCTCTTTTGTTTACTCAACCGCTACTTTAGACTGACTCTTG +GTGTTTATGATTACTTAGTTTCTACACAGGAGTTTAGATATATGAATTCACAGGGACTACTCCCACCCAA +GAATAGCATAGATGCCTTCAAACTCAACATTAAATTGTTGGGTGTTGGTGGCAAACCTTGTATCAAAGTA +GCCACTGTACAGTCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAAC +TCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAA +AGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTA +GACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAAGCTATAGCCTCAGAGTTTA +GTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGA +TTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCA +GCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTG +AGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAA +TGATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACA +ACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACAT +TTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAG +TGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCT +GCTGTCAAATTACAGAATAATGAGCTTAGTCCTGTTGCACTACGACAGATGTCTTGTGCTGCCGGTACTA +CACAAACTGCTTGCACTGATGACAATGCGTTAGCTTACTACAACACAACAAAGGGAGGTAGGTTTGTACT +TGCACTGTTATCCGATTTACAGGATTTGAAATGGGCTAGATTCCCTAAGAGTGATGGAACTGGTACTATC +TATACAGAACTGGAACCACCTTGTAGGTTTGTTACAGACACACCTAAAGGTCCTAAAGTGAAGTATTTAT +ACTTTATTAAAGGATTAAACAACCTAAATAGAGGTATGGTACTTGGTAGTTTAGCTGCCACAGTACGTCT +ACAAGCTGGTAATGCAACAGAAGTGCCTGCCAATTCAACTGTATTATCTTTCTGTGCTTTTGCTGTAGAT +GCTGCTAAAGCTTACAAAGATTATCTAGCTAGTGGGGGACAACCAATCACTAATTGTGTTAAGATGTTGT +GTACACACACTGGTACTGGTCAGGCAATAACAGTTACACCGGAAGCCAATATGGATCAAGAATCCTTTGG +TGGTGCATCGTGTTGTCTGTACTGCCGTTGCCACATAGATCATCCAAATCCTAAAGGATTTTGTGACTTA +AAAGGTAAGTATGTACAAATACCTACAACTTGTGCTAATGACCCTGTGGGTTTTACACTTAAAAACACAG +TCTGTACCGTCTGCGGTATGTGGAAAGGTTATGGCTGTAGTTGTGATCAACTCCGCGAACCCATGCTTCA +GTCAGCTGATGCACAATCGTTTTTAAACGGGTTTGCGGTGTAAGTGCAGCCCGTCTTACACCGTGCGGCA +CAGGCACTAGTACTGATGTCGTATACAGGGCTTTTGACATCTACAATGATAAAGTAGCTGGTTTTGCTAA +ATTCCTAAAAACTAATTGTTGTCGCTTCCAAGAAAAGGACGAAGATGACAATTTAATTGATTCTTACTTT +GTAGTTAAGAGACACACTTTCTCTAACTACCAACATGAAGAAACAATTTATAATTTACTTAAGGATTGTC +CAGCTGTTGCTAAACATGACTTCTTTAAGTTTAGAATAGACGGTGACATGGTACCACATATATCACGTCA +ACGTCTTACTAAATACACAATGGCAGACCTCGTCTATGCTTTAAGGCATTTTGATGAAGGTAATTGTGAC +ACATTAAAAGAAATACTTGTCACATACAATTGTTGTGATGATGATTATTTCAATAAAAAGGACTGGTATG +ATTTTGTAGAAAACCCAGATATATTACGCGTATACGCCAACTTAGGTGAACGTGTACGCCAAGCTTTGTT +AAAAACAGTACAATTCTGTGATGCCATGCGAAATGCTGGTATTGTTGGTGTACTGACATTAGATAATCAA +GATCTCAATGGTAACTGGTATGATTTCGGTGATTTCATACAAACCACGCCAGGTAGTGGAGTTCCTGTTG +TAGATTCTTATTATTCATTGTTAATGCCTATATTAACCTTGACCAGGGCTTTAACTGCAGAGTCACATGT +TGACACTGACTTAACAAAGCCTTACATTAAGTGGGATTTGTTAAAATATGACTTCACGGAAGAGAGGTTA +AAACTCTTTGACCGTTATTTTAAATATTGGGATCAGACATACCACCCAAATTGTGTTAACTGTTTGGATG +ACAGATGCATTCTGCATTGTGCAAACTTTAATGTTTTATTCTCTACAGTGTTCCCACCTACAAGTTTTGG +ACCACTAGTGAGAAAAATATTTGTTGATGGTGTTCCATTTGTAGTTTCAACTGGATACCACTTCAGAGAG +CTAGGTGTTGTACATAATCAGGATGTAAACTTACATAGCTCTAGACTTAGTTTTAAGGAATTACTTGTGT +ATGCTGCTGACCCTGCTATGCACGCTGCTTCTGGTAATCTATTACTAGATAAACGCACTACGTGCTTTTC +AGTAGCTGCACTTACTAACAATGTTGCTTTTCAAACTGTCAAACCCGGTAATTTTAACAAAGACTTCTAT +GACTTTGCTGTGTCTAAGGGTTTCTTTAAGGAAGGAAGTTCTGTTGAATTAAAACACTTCTTCTTTGCTC +AGGATGGTAATGCTGCTATCAGCGATTATGACTACTATCGTTATAATCTACCAACAATGTGTGATATCAG +ACAACTACTATTTGTAGTTGAAGTTGTTGATAAGTACTTTGATTGTTACGATGGTGGCTGTATTAATGCT +AACCAAGTCATCGTCAACAACCTAGACAAATCAGCTGGTTTTCCATTTAATAAATGGGGTAAGGCTAGAC +TTTATTATGATTCAATGAGTTATGAGGATCAAGATGCACTTTTCGCATATACAAAACGTAATGTCATCCC +TACTATAACTCAAATGAATCTTAAGTATGCCATTAGTGCAAAGAATAGAGCTCGCACCGTAGCTGGTGTC +TCTATCTGTAGTACTATGACCAATAGACAGTTTCATCAAAAATTATTGAAATCAATAGCCGCCACTAGAG +GAGCTACTGTAGTAATTGGAACAAGCAAATTCTATGGTGGTTGGCACAACATGTTAAAAACTGTTTATAG +TGATGTAGAAAACCCTCACCTTATGGGTTGGGATTATCCTAAATGTGATAGAGCCATGCCTAACATGCTT +AGAATTATGGCCTCACTTGTTCTTGCTCGCAAACATACAACGTGTTGTAGCTTGTCACACCGTTTCTATA +GATTAGCTAATGAGTGTGCTCAAGTATTGAGTGAAATGGTCATGTGTGGCGGTTCACTATATGTTAAACC +AGGTGGAACCTCATCAGGAGATGCCACAACTGCTTATGCTAATAGTGTTTTTAACATTTGTCAAGCTGTC +ACGGCCAATGTTAATGCACTTTTATCTACTGATGGTAACAAAATTGCCGATAAGTATGTCCGCAATTTAC +AACACAGACTTTATGAGTGTCTCTATAGAAATAGAGATGTTGACACAGACTTTGTGAATGAGTTTTACGC +ATATTTGCGTAAACATTTCTCAATGATGATACTCTCTGACGATGCTGTTGTGTGTTTCAATAGCACTTAT +GCATCTCAAGGTCTAGTGGCTAGCATAAAGAACTTTAAGTCAGTTCTTTATTATCAAAACAATGTTTTTA +TGTCTGAAGCAAAATGTTGGACTGAGACTGACCTTACTAAAGGACCTCATGAATTTTGCTCTCAACATAC +AATGCTAGTTAAACAGGGTGATGATTATGTGTACCTTCCTTACCCAGATCCATCAAGAATCCTAGGGGCC +GGCTGTTTTGTAGATGATATCGTAAAAACAGATGGTACACTTATGATTGAACGGTTCGTGTCTTTAGCTA +TAGATGCTTACCCACTTACTAAACATCCTAATCAGGAGTATGCTGATGTCTTTCATTTGTACTTACAATA +CATAAGAAAGCTACATGATGAGTTAACAGGACACATGTTAGACATGTATTCTGTTATGCTTACTAATGAT +AACACTTCAAGGTATTGGGAACCTGAGTTTTATGAGGCTATGTACACACCGCATACAGTCTTACAGGCTG +TTGGGGCTTGTGTTCTTTGCAATTCACAGACTTCATTAAGATGTGGTGCTTGCATACGTAGACCATTCTT +ATGTTGTAAATGCTGTTACGACCATGTCATATCAACATCACATAAATTAGTCTTGTCTGTTAATCCGTAT +GTTTGCAATGCTCCAGGTTGTGATGTCACAGATGTGACTCAACTTTACTTAGGAGGTATGAGCTATTATT +GTAAATCACATAAACCACCCATTAGTTTTCCATTGTGTGCTAATGGACAAGTTTTTGGTTTATATAAAAA +TACATGTGTTGGTAGCGATAATGTTACTGACTTTAATGCAATTGCAACATGTGACTGGACAAATGCTGGT +GATTACATTTTAGCTAACACCTGTACTGAAAGACTCAAGCTTTTTGCAGCAGAAACGCTCAAAGCTACTG +AGGAGACATTTAAACTGTCTTATGGTATTGCTACTGTACGTGAAGTGCTGTCTGACAGAGAATTACATCT +TTCATGGGAAGTTGGTAAACCTAGACCACCACTTAACCGAAATTATGTCTTTACTGGTTATCGTGTAACT +AAAAACAGTAAAGTACAAATAGGAGAGTACACCTTTGAAAAAGGTGACTATGGTGATGCTGTTGTTTACC +GAGGTACAACAACTTACAAATTAAATGTTGGTGATTATTTTGTGCTGACATCACATACAGTAATGCCATT +AAGTGCACCTACACTAGTGCCACAAGAGCACTATGTTAGAATTACTGGCTTATACCCAACACTCAATATC +TCAGATGAGTTTTCTAGCAATGTTGCAAATTATCAAAAGGTTGGTATGCAAAAGTATTCTACACTCCAGG +GACCACCTGGTACTGGTAAGAGTCATTTTGCTATTGGCCTAGCTCTCTACTACCCTTCTGCTCGCATAGT +GTATACAGCTTGCTCTCATGCCGCTGTTGATGCACTATGTGAGAAGGCATTAAAATATTTGCCTATAGAT +AAATGTAGTAGAATTATACCTGCACGTGCTCGTGTAGAGTGTTTTGATAAATTCAAAGTGAATTCAACAT +TAGAACAGTATGTCTTTTGTACTGTAAATGCATTGCCTGAGACGACAGCAGATATAGTTGTCTTTGATGA +AATTTCAATGGCCACAAATTATGATTTGAGTGTTGTCAATGCCAGATTACGTGCTAAGCACTATGTGTAC +ATTGGCGACCCTGCTCAATTACCTGCACCACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATT +TCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCC +TGCTGAAATTGTTGACACTGTGAGTGCTTTGGTTTATGATAATAAGCTTAAAGCACATAAAGACAAATCA +GCTCAATGCTTTAAAATGTTTTATAAGGGTGTTATCACGCATGATGTTTCATCTGCAATTAACAGGCCAC +AAATAGGCGTGGTAAGAGAATTCCTTACACGTAACCCTGCTTGGAGAAAAGCTGTCTTTATTTCACCTTA +TAATTCACAGAATGCTGTAGCCTCAAAGATTTTGGGACTACCAACTCAAACTGTTGATTCATCACAGGGC +TCAGAATATGACTATGTCATATTCACTCAAACCACTGAAACAGCTCACTCTTGTAATGTAAACAGATTTA +ATGTTGCTATTACCAGAGCAAAAGTAGGCATACTTTGCATAATGTCTGATAGAGACCTTTATGACAAGTT +GCAATTTACAAGTCTTGAAATTCCACGTAGGAATGTGGCAACTTTACAAGCTGAAAATGTAACAGGACTC +TTTAAAGATTGTAGTAAGGTAATCACTGGGTTACATCCTACACAGGCACCTACACACCTCAGTGTTGACA +CTAAATTCAAAACTGAAGGTTTATGTGTTGACATACCTGGCATACCTAAGGACATGACCTATAGAAGACT +CATCTCTATGATGGGTTTTAAAATGAATTATCAAGTTAATGGTTACCCTAACATGTTTATCACCCGCGAA +GAAGCTATAAGACATGTACGTGCATGGATTGGCTTCGATGTCGAGGGGTGTCATGCTACTAGAGAAGCTG +TTGGTACCAATTTACCTTTACAGCTAGGTTTTTCTACAGGTGTTAACCTAGTTGCTGTACCTACAGGTTA +TGTTGATACACCTAATAATACAGATTTTTCCAGAGTTAGTGCTAAACCACCGCCTGGAGATCAATTTAAA +CACCTCATACCACTTATGTACAAAGGACTTCCTTGGAATGTAGTGCGTATAAAGATTGTACAAATGTTAA +GTGACACACTTAAAAATCTCTCTGACAGAGTCGTATTTGTCTTATGGGCACATGGCTTTGAGTTGACATC +TATGAAGTATTTTGTGAAAATAGGACCTGAGCGCACCTGTTGTCTATGTGATAGACGTGCCACATGCTTT +TCCACTGCTTCAGACACTTATGCCTGTTGGCATCATTCTATTGGATTTGATTACGTCTATAATCCGTTTA +TGATTGATGTTCAACAATGGGGTTTTACAGGTAACCTACAAAGCAACCATGATCTGTATTGTCAAGTCCA +TGGTAATGCACATGTAGCTAGTTGTGATGCAATCATGACTAGGTGTCTAGCTGTCCACGAGTGCTTTGTT +AAGCGTGTTGACTGGACTATTGAATATCCTATAATTGGTGATGAACTGAAGATTAATGCGGCTTGTAGAA +AGGTTCAACACATGGTTGTTAAAGCTGCATTATTAGCAGACAAATTCCCAGTTCTTCACGACATTGGTAA +CCCTAAAGCTATTAAGTGTGTACCTCAAGCTGATGTAGAATGGAAGTTCTATGATGCACAGCCTTGTAGT +GACAAAGCTTATAAAATAGAAGAATTATTCTATTCTTATGCCACACATTCTGACAAATTCACAGATGGTG +TATGCCTATTTTGGAATTGCAATGTCGATAGATATCCTGCTAATTCCATTGTTTGTAGATTTGACACTAG +AGTGCTATCTAACCTTAACTTGCCTGGTTGTGATGGTGGCAGTTTGTATGTAAATAAACATGCATTCCAC +ACACCAGCTTTTGATAAAAGTGCTTTTGTTAATTTAAAACAATTACCATTTTTCTATTACTCTGACAGTC +CATGTGAGTCTCATGGAAAACAAGTAGTGTCAGATATAGATTATGTACCACTAAAGTCTGCTACGTGTAT +AACACGTTGCAATTTAGGTGGTGCTGTCTGTAGACATCATGCTAATGAGTACAGATTGTATCTCGATGCT +TATAACATGATGATCTCAGCTGGCTTTAGCTTGTGGGTTTACAAACAATTTGATACTTATAACCTCTGGA +ACACTTTTACAAGACTTCAGAGTTTAGAAAATGTGGCTTTTAATGTTGTAAATAAGGGACACTTTGATGG +ACAACAGGGTGAAGTACCAGTTTCTATCATTAATAACACTGTTTACACAAAAGTTGATGGTGTTGATGTA +GAATTGTTTGAAAATAAAACAACATTACCTGTTAATGTAGCATTTGAGCTTTGGGCTAAGCGCAACATTA +AACCAGTACCAGAGGTGAAAATACTCAATAATTTGGGTGTGGACATTGCTGCTAATACTGTGATCTGGGA +CTACAAAAGAGATGCTCCAGCACATATATCTACTATTGGTGTTTGTTCTATGACTGACATAGCCAAGAAA +CCAACTGAAACGATTTGTGCACCACTCACTGTCTTTTTTGATGGTAGAGTTGATGGTCAAGTAGACTTAT +TTAGAAATGCCCGTAATGGTGTTCTTATTACAGAAGGTAGTGTTAAAGGTTTACAACCATCTGTAGGTCC +CAAACAAGCTAGTCTTAATGGAGTCACATTAATTGGAGAAGCCGTAAAAACACAGTTCAATTATTATAAG +AAAGTTGATGGTGTTGTCCAACAATTACCTGAAACTTACTTTACTCAGAGTAGAAATTTACAAGAATTTA +AACCCAGGAGTCAAATGGAAATTGATTTCTTAGAATTAGCTATGGATGAATTCATTGAACGGTATAAATT +AGAAGGCTATGCCTTCGAACATATCGTTTATGGAGATTTTAGTCATAGTCAGTTAGGTGGTTTACATCTA +CTGATTGGACTAGCTAAACGTTTTAAGGAATCACCTTTTGAATTAGAAGATTTTATTCCTATGGACAGTA +CAGTTAAAAACTATTTCATAACAGATGCGCAAACAGGTTCATCTAAGTGTGTGTGTTCTGTTATTGATTT +ATTACTTGATGATTTTGTTGAAATAATAAAATCCCAAGATTTATCTGTAGTTTCTAAGGTTGTCAAAGTG +ACTATTGACTATACAGAAATTTCATTTATGCTTTGGTGTAAAGATGGCCATGTAGAAACATTTTACCCAA +AATTACAATCTAGTCAAGCGTGGCAACCGGGTGTTGCTATGCCTAATCTTTACAAAATGCAAAGAATGCT +ATTAGAAAAGTGTGACCTTCAAAATTATGGTGATAGTGCAACATTACCTAAAGGCATAATGATGAATGTC +GCAAAATATACTCAACTGTGTCAATATTTAAACACATTAACATTAGCTGTACCCTATAATATGAGAGTTA +TACATTTTGGTGCTGGTTCTGATAAAGGAGTTGCACCAGGTACAGCTGTTTTAAGACAGTGGTTGCCTAC +GGGTACGCTGCTTGTCGATTCAGATCTTAATGACTTTGTCTCTGATGCAGATTCAACTTTGATTGGTGAT +TGTGCAACTGTACATACAGCTAATAAATGGGATCTCATTATTAGTGATATGTACGACCCTAAGACTAAAA +ATGTTACAAAAGAAAATGACTCTAAAGAGGGTTTTTTCACTTACATTTGTGGGTTTATACAACAAAAGCT +AGCTCTTGGAGGTTCCGTGGCTATAAAGATAACAGAACATTCTTGGAATGCTGATCTTTATAAGCTCATG +GGACACTTCGCATGGTGGACAGCCTTTGTTACTAATGTGAATGCGTCATCATCTGAAGCATTTTTAATTG +GATGTAATTATCTTGGCAAACCACGCGAACAAATAGATGGTTATGTCATGCATGCAAATTACATATTTTG +GAGGAATACAAATCCAATTCAGTTGTCTTCCTATTCTTTATTTGACATGAGTAAATTTCCCCTTAAATTA +AGGGGTACTGCTGTTATGTCTTTAAAAGAAGGTCAAATCAATGATATGATTTTATCTCTTCTTAGTAAAG +GTAGACTTATAATTAGAGAAAACAACAGAGTTGTTATTTCTAGTGATGTTCTTGTTAACAACTAAACGAA +CAATGTTTGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACCAGAACTCA +ATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGACAAAGTTTTCAGATCCTCA +GTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCCAATGTTACTTGGTTCCATGCTATACATG +TCTCTGGGACCAATGGTACTAAGAGGTTTGATAACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGC +TTCCACTGAGAAGTCTAACATAATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCC +CTACTTATTGTTAATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATGATCCAT +TTTTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTATTCTAGTGC +GAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAAGGAAAACAGGGTAATTTC +AAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTATTTTAAAATATATTCTAAGCACACGCCTA +TTAATTTAGTGCGTGATCTCCCTCAGGGTTTTTCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTAT +TAACATCACTAGGTTTCAAACTTTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCA +GGTTGGACAGCTGGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATA +ATGAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAGTGTACGTT +GAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTCCAACCAACAGAATCTATT +GTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAAGTTTTTAACGCCACCAGATTTGCATCTG +TTTATGCTTGGAACAGGAAGAGAATCAGCAACTGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATC +ATTTTCCACTTTTAAGTGTTATGGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTAT +GCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTG +ATTATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAATCTTGATTC +TAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAATCTCAAACCTTTTGAGAGA +GATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGTAATGGTGTTGAAGGTTTTAATTGTTACT +TTCCTTTACAATCATATGGTTTCCAACCCACTAATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACT +TTCTTTTGAACTTCTACATGCACCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAAC +AAATGTGTCAATTTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTC +TGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAGACACTTGA +GATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCAGGAACAAATACTTCTAAC +CAGGTTGCTGTTCTTTATCAGGATGTTAACTGCACAGAAGTCCCTGTTGCTATTCATGCAGATCAACTTA +CTCCTACTTGGCGTGTTTATTCTACAGGTTCTAATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGC +TGAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACT +CAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTG +GTGCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATTAGTGTTAC +CACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATGTACATTTGTGGTGATTCA +ACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGTACACAATTAAACCGTGCTTTAACTGGAA +TAGCTGTTGAACAAGACAAAAACACCCAAGAAGTTTTTGCACAAGTCAAACAAATTTACAAAACACCACC +AATTAAAGATTTTGGTGGTTTTAATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCA +TTTATTGAAGATCTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATT +GCCTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTTTTGCCACC +TTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGTACAATCACTTCTGGTTGG +ACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATGCAAATGGCTTATAGGTTTAATGGTATTG +GAGTTACACAGAATGTTCTCTATGAGAACCAAAAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAA +AATTCAAGACTCACTTTCTTCCACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCA +CAAGCTTTAAACACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATA +TCCTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGACTTCAAAG +TTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCTTCTGCTAATCTTGCTGCT +ACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTTGATTTTTGTGGAAAGGGCTATCATCTTA +TGTCCTTCCCTCAGTCAGCACCTCATGGTGTAGTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAA +GAACTTCACAACTGCTCCTGCCATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTT +TCAAATGGCACACACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACA +CATTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCTTTGCAACC +TGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACATCACCAGATGTTGATTTA +GGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAAAAAGAAATTGACCGCCTCAATGAGGTTG +CCAAGAATTTAAATGAATCTCTCATCGATCTCCAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCC +ATGGTACATTTGGCTAGGTTTTATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGT +ATGACCAGTTGCTGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACG +ACTCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACATAAACGAACTTATGGATTTGTTTATGAGA +ATCTTCACAATTGGAACTGTAACTTTGAAGCAAGGTGAAATCAAGGATGCTACTCCTTCAGATTTTGTTC +GCGCTACTGCAACGATACCGATACAAGCCTCACTCCCTTTCGGATGGCTTATTGTTGGCGTTGCACTTCT +TGCTGTTTTTCAGAGCGCTTCCAAAATCATAACCCTCAAAAAGAGATGGCAACTAGCACTCTCCAAGGGT +GTTCACTTTGTTTGCAACTTGCTGTTGTTGTTTGTAACAGTTTACTCACACCTTTTGCTCGTTGCTGCTG +GCCTTGAAGCCCCTTTTCTCTATCTTTATGCTTTAGTCTACTTCTTGCAGAGTATAAACTTTGTAAGAAT +AATAATGAGGCTTTGGCTTTGCTGGAAATGCCGTTCCAAAAACCCATTACTTTATGATGCCAACTATTTT +CTTTGCTGGCATACTAATTGTTACGACTATTGTATACCTTACAATAGTGTAACTTCTTCAATTGTCATTA +CTTCAGGTGATGGCACAACAAGTCCTATTTCTGAACATGACTACCAGATTGGTGGTTATACTGAAAAATG +GGAATCTGGAGTAAAAGACTGTGTTGTATTACACAGTTACTTCACTTCAGACTATTACCAGCTGTACTCA +ACTCAATTGAGTACAGACACTGGTGTTGAACATGTTACCTTCTTCATCTACAATAAAATTGTTGATGAGC +CTGAAGAACATGTCCAAATTCACACAATCGACGGTTCATCCGGAGTTGTTAATCCAGTAATGGAACCAAT +TTATGATGAACCGACGACGACTACTAGCGTGCCTTTGTAAGCACAAGCTGATGAGTACGAACTTATGTAC +TCATTCGTTTCGGAAGAGACAGGTACGTTAATAGTTAATAGCGTACTTCTTTTTCTTGCTTTCGTGGTAT +TCTTGCTAGTTACACTAGCCATCCTTACTGCGCTTCGATTGTGTGCGTACTGCTGCAATATTGTTAACGT +GAGTCTTGTAAAACCTTCTTTTTACGTTTACTCTCGTGTTAAAAATCTGAATTCTTCTAGAGTTCCTGAT +CTTCTGGTCTAAACGAACTAAATATTATATTAGTTTTTCTGTTTGGAACTTTAATTTTAGCCATGGCAGA +TTCCAACGGTACTATTACCGTTGAAGAGCTTAAAAAGCTCCTTGAACAATGGAACCTAGTAATAGGTTTC +CTATTCCTTACATGGATTTGTCTTCTACAATTTGCCTATGCCAACAGGAATAGGTTTTTGTATATAATTA +AGTTAATTTTCCTCTGGCTGTTATGGCCAGTAACTTTAGCTTGTTTTGTGCTTGCTGCTGTTTACAGAAT +AAATTGGATCACCGGTGGAATTGCTATCGCAATGGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTC +ATTGCTTCTTTCAGACTGTTTGCGCGTACGCGTTCCATGTGGTCATTCAATCCAGAAACTAACATTCTTC +TCAACGTGCCACTCCATGGCACTATTCTGACCAGACCGCTTCTAGAAAGTGAACTCGTAATCGGAGCTGT +GATCCTTCGTGGACATCTTCGTATTGCTGGACACCATCTAGGACGCTGTGACATCAAGGACCTGCCTAAA +GAAATCACTGTTGCTACATCACGAACGCTTTCTTATTACAAATTGGGAGCTTCGCAGCGTGTAGCAGGTG +ACTCAGGTTTTGCTGCATACAGTCGCTACAGGATTGGCAACTATAAATTAAACACAGACCATTCCAGTAG +CAGTGACAATATTGCTTTGCTTGTACAGTAAGTGACAACAGATGTTTCATCTCGTTGACTTTCAGGTTAC +TATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATA +AACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAAC +CAATGGAGATTGATTAAACGAACATGAAAATTATTCTTTTCTTGGCACTGATAACACTCGCTACTTGTGA +GCTTTATCACTACCAAGAGTGTGTTAGAGGTACAACAGTACTTTTAAAAGAACCTTGCTCTTCTGGAACA +TACGAGGGCAATTCACCATTTCATCCTCTAGCTGATAACAAATTTGCACTGACTTGCTTTAGCACTCAAT +TTGCTTTTGCTTGTCCTGACGGCGTAAAACACGTCTATCAGTTACGTGCCAGATCAGTTTCACCTAAACT +GTTCATCAGACAAGAGGAAGTTCAAGAACTTTACTCTCCAATTTTTCTTATTGTTGCGGCAATAGTGTTT +ATAACACTTTGCTTCACACTCAAAAGAAAGACAGAATGATTGAACTTTCATTAATTGACTTCTATTTGTG +CTTTTTAGCCTTTCTGCTATTCCTTGTTTTAATTATGCTTATTATCTTTTGGTTCTCACTTGAACTGCAA +GATCATAATGAAACTTGTCACGCCTAAACGAACATGAAATTTCTTGTTTTCTTAGGAATCATCACAACTG +TAGCTGCATTTCACCAAGAATGTAGTTTACAGTCATGTACTCAACATCAACCATATGTAGTTGATGACCC +GTGTCCTATTCACTTCTATTCTAAATGGTATATTAGAGTAGGAGCTAGAAAATCAGCACCTTTAATTGAA +TTGTGCGTGGATGAGGCTGGTTCTAAATCACCCATTCAGTACATCGATATCGGTAATTATACAGTTTCCT +GTTTACCTTTTACAATTAATTGCCAGGAACCTAAATTGGGTAGTCTTGTAGTGCGTTGTTCGTTCTATGA +AGACTTTTTAGAGTATCATGACGTTCGTGTTGTTTTAGATTTCATCTAAACGAACAAACTAAAATGTCTG +ATAATGGACCCCAAAATCAGCGAAATGCACCCCGCATTACGTTTGGTGGACCCTCAGATTCAACTGGCAG +TAACCAGAATGGAGAACGCAGTGGGGCGCGATCAAAACAACGTCGGCCCCAAGGTTTACCCAATAATACT +GCGTCTTGGTTCACCGCTCTCACTCAACATGGCAAGGAAGACCTTAAATTCCCTCGAGGACAAGGCGTTC +CAATTAACACCAATAGCAGTCCAGATGACCAAATTGGCTACTACCGAAGAGCTACCAGACGAATTCGTGG +TGGTGACGGTAAAATGAAAGATCTCAGTCCAAGATGGTATTTCTACTACCTAGGAACTGGGCCAGAAGCT +GGACTTCCCTATGGTGCTAACAAAGACGGCATCATATGGGTTGCAACTGAGGGAGCCTTGAATACACCAA +AAGATCACATTGGCACCCGCAATCCTGCTAACAATGCTGCAATCGTGCTACAACTTCCTCAAGGAACAAC +ATTGCCAAAAGGCTTCTACGCAGAAGGGAGCAGAGGCGGCAGTCAAGCCTCTTCTCGTTCCTCATCACGT +AGTCGCAACAGTTCAAGAAATTCAACTCCAGGCAGCAGTAGGGGAACTTCTCCTGCTAGAATGGCTGGCA +ATGGCGGTGATGCTGCTCTTGCTTTGCTGCTGCTTGACAGATTGAACCAGCTTGAGAGCAAAATGTCTGG +TAAAGGCCAACAACAACAAGGCCAAACTGTCACTAAGAAATCTGCTGCTGAGGCTTCTAAGAAGCCTCGG +CAAAAACGTACTGCCACTAAAGCATACAATGTAACACAAGCTTTCGGCAGACGTGGTCCAGAACAAACCC +AAGGAAATTTTGGGGACCAGGAACTAATCAGACAAGGAACTGATTACAAACATTGGCCGCAAATTGCACA +ATTTGCCCCCAGCGCTTCAGCGTTCTTCGGAATGTCGCGCATTGGCATGGAAGTCACACCTTCGGGAACG +TGGTTGACCTACACAGGTGCCATCAAATTGGATGACAAAGATCCAAATTTCAAAGATCAAGTCATTTTGC +TGAATAAGCATATTGACGCATACAAAACATTCCCACCAACAGAGCCTAAAAAGGACAAAAAGAAGAAGGC +TGATGAAACTCAAGCCTTACCGCAGAGACAGAAGAAACAGCAAACTGTGACTCTTCTTCCTGCTGCAGAT +TTGGATGATTTCTCCAAACAATTGCAACAATCCATGAGCAGTGCTGACTCAACTCAGGCCTAAACTCATG +CAGACCACACAAGGCAGATGGGCTATATAAACGTTTTCGCTTTTCCGTTTACGATATATAGTCTACTCTT +GTGCAGAATGAATTCTCGTAACTACATAGCACAAGTAGATGTAGTTAACTTTAATCTCACATAGCAATCT +TTAATCAGTGTGTAACATTAGGGAGGACTTGAAAGAGCCACCACATTTTCACCGAGGCCACGCGGAGTAC +GATCGAGTGTACAGTGAACAATGCTAGGGAGAGCTGCCTATATGGAAGAGCCCTAATGTGTAAAATTAAT +TTTAGTAGTGCTATCCCCATGTGATTTTAATAGCTTCTTAGGAGAATGACAAAAAAAAAAAAAAAAAAAA +AAAAAAAAAAAAA diff --git a/test/data/primer-schemes/schemes/sars-cov-2/artic/400/v4.1.0/scheme.bed b/test/data/primer-schemes/schemes/sars-cov-2/artic/400/v4.1.0/scheme.bed new file mode 100644 index 0000000..037a691 --- /dev/null +++ b/test/data/primer-schemes/schemes/sars-cov-2/artic/400/v4.1.0/scheme.bed @@ -0,0 +1,209 @@ +MN908947.3 25 50 SARS-CoV-2_1_LEFT_1 1 + +MN908947.3 408 431 SARS-CoV-2_1_RIGHT_1 1 - +MN908947.3 324 344 SARS-CoV-2_2_LEFT_1 2 + +MN908947.3 705 727 SARS-CoV-2_2_RIGHT_1 2 - +MN908947.3 644 666 SARS-CoV-2_3_LEFT_1 1 + +MN908947.3 1017 1044 SARS-CoV-2_3_RIGHT_1 1 - +MN908947.3 944 966 SARS-CoV-2_4_LEFT_1 2 + +MN908947.3 1337 1362 SARS-CoV-2_4_RIGHT_1 2 - +MN908947.3 1245 1266 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10491 SARS-CoV-2_34_RIGHT_1 2 - +MN908947.3 10393 10419 SARS-CoV-2_35_LEFT_1 1 + +MN908947.3 10785 10810 SARS-CoV-2_35_RIGHT_1 1 - +MN908947.3 10713 10742 SARS-CoV-2_36_LEFT_1 2 + +MN908947.3 11092 11116 SARS-CoV-2_36_RIGHT_1 2 - +MN908947.3 11000 11023 SARS-CoV-2_37_LEFT_1 1 + +MN908947.3 11388 11414 SARS-CoV-2_37_RIGHT_1 1 - +MN908947.3 11305 11330 SARS-CoV-2_38_LEFT_1 2 + +MN908947.3 11689 11720 SARS-CoV-2_38_RIGHT_1 2 - +MN908947.3 11624 11651 SARS-CoV-2_39_LEFT_1 1 + +MN908947.3 12011 12033 SARS-CoV-2_39_RIGHT_1 1 - +MN908947.3 11937 11963 SARS-CoV-2_40_LEFT_1 2 + +MN908947.3 12317 12339 SARS-CoV-2_40_RIGHT_1 2 - +MN908947.3 12234 12255 SARS-CoV-2_41_LEFT_1 1 + +MN908947.3 12618 12643 SARS-CoV-2_41_RIGHT_1 1 - +MN908947.3 12519 12546 SARS-CoV-2_42_LEFT_1 2 + +MN908947.3 12895 12920 SARS-CoV-2_42_RIGHT_1 2 - +MN908947.3 12831 12856 SARS-CoV-2_43_LEFT_1 1 + +MN908947.3 13218 13240 SARS-CoV-2_43_RIGHT_1 1 - +MN908947.3 13124 13148 SARS-CoV-2_44_LEFT_1 2 + +MN908947.3 13506 13528 SARS-CoV-2_44_RIGHT_1 2 - +MN908947.3 13463 13485 SARS-CoV-2_45_LEFT_1 1 + +MN908947.3 13833 13859 SARS-CoV-2_45_RIGHT_1 1 - +MN908947.3 13752 13775 SARS-CoV-2_46_LEFT_1 2 + +MN908947.3 14120 14144 SARS-CoV-2_46_RIGHT_1 2 - +MN908947.3 14045 14075 SARS-CoV-2_47_LEFT_1 1 + +MN908947.3 14428 14457 SARS-CoV-2_47_RIGHT_1 1 - +MN908947.3 14338 14362 SARS-CoV-2_48_LEFT_1 2 + +MN908947.3 14717 14743 SARS-CoV-2_48_RIGHT_1 2 - +MN908947.3 14647 14674 SARS-CoV-2_49_LEFT_1 1 + +MN908947.3 15023 15050 SARS-CoV-2_49_RIGHT_1 1 - +MN908947.3 14953 14983 SARS-CoV-2_50_LEFT_1 2 + +MN908947.3 15336 15358 SARS-CoV-2_50_RIGHT_1 2 - +MN908947.3 15214 15237 SARS-CoV-2_51_LEFT_1 1 + +MN908947.3 15596 15619 SARS-CoV-2_51_RIGHT_1 1 - +MN908947.3 15535 15557 SARS-CoV-2_52_LEFT_1 2 + +MN908947.3 15917 15941 SARS-CoV-2_52_RIGHT_1 2 - +MN908947.3 15855 15881 SARS-CoV-2_53_LEFT_1 1 + +MN908947.3 16239 16260 SARS-CoV-2_53_RIGHT_1 1 - +MN908947.3 16112 16137 SARS-CoV-2_54_LEFT_1 2 + +MN908947.3 16483 16508 SARS-CoV-2_54_RIGHT_1 2 - +MN908947.3 16386 16408 SARS-CoV-2_55_LEFT_1 1 + +MN908947.3 16767 16796 SARS-CoV-2_55_RIGHT_1 1 - +MN908947.3 16692 16714 SARS-CoV-2_56_LEFT_1 2 + +MN908947.3 17082 17105 SARS-CoV-2_56_RIGHT_1 2 - +MN908947.3 16986 17013 SARS-CoV-2_57_LEFT_1 1 + +MN908947.3 17381 17405 SARS-CoV-2_57_RIGHT_1 1 - +MN908947.3 17323 17345 SARS-CoV-2_58_LEFT_1 2 + +MN908947.3 17688 17711 SARS-CoV-2_58_RIGHT_1 2 - +MN908947.3 17615 17642 SARS-CoV-2_59_LEFT_1 1 + +MN908947.3 17997 18022 SARS-CoV-2_59_RIGHT_1 1 - +MN908947.3 17911 17939 SARS-CoV-2_60_LEFT_1 2 + +MN908947.3 18307 18328 SARS-CoV-2_60_RIGHT_1 2 - +MN908947.3 18244 18267 SARS-CoV-2_61_LEFT_1 1 + +MN908947.3 18624 18652 SARS-CoV-2_61_RIGHT_1 1 - +MN908947.3 18550 18578 SARS-CoV-2_62_LEFT_1 2 + +MN908947.3 18936 18961 SARS-CoV-2_62_RIGHT_1 2 - +MN908947.3 18869 18891 SARS-CoV-2_63_LEFT_1 1 + +MN908947.3 19252 19277 SARS-CoV-2_63_RIGHT_1 1 - +MN908947.3 19183 19208 SARS-CoV-2_64_LEFT_1 2 + +MN908947.3 19558 19586 SARS-CoV-2_64_RIGHT_1 2 - +MN908947.3 19485 19513 SARS-CoV-2_65_LEFT_1 1 + +MN908947.3 19877 19901 SARS-CoV-2_65_RIGHT_1 1 - +MN908947.3 19810 19836 SARS-CoV-2_66_LEFT_1 2 + +MN908947.3 20186 20216 SARS-CoV-2_66_RIGHT_1 2 - +MN908947.3 20090 20117 SARS-CoV-2_67_LEFT_1 1 + +MN908947.3 20472 20497 SARS-CoV-2_67_RIGHT_1 1 - +MN908947.3 20377 20405 SARS-CoV-2_68_LEFT_1 2 + +MN908947.3 20766 20792 SARS-CoV-2_68_RIGHT_1 2 - +MN908947.3 20677 20699 SARS-CoV-2_69_LEFT_1 1 + +MN908947.3 21050 21080 SARS-CoV-2_69_RIGHT_1 1 - +MN908947.3 20988 21013 SARS-CoV-2_70_LEFT_1 2 + +MN908947.3 21358 21387 SARS-CoV-2_70_RIGHT_1 2 - +MN908947.3 21294 21316 SARS-CoV-2_71_LEFT_1 1 + +MN908947.3 21675 21700 SARS-CoV-2_71_RIGHT_1 1 - +MN908947.3 21532 21561 SARS-CoV-2_72_LEFT_1 2 + +MN908947.3 21904 21933 SARS-CoV-2_72_RIGHT_1 2 - +MN908947.3 21865 21889 SARS-CoV-2_73_LEFT_1 1 + +MN908947.3 22247 22274 SARS-CoV-2_73_RIGHT_1 1 - +MN908947.3 22091 22113 SARS-CoV-2_74_LEFT_1 2 + +MN908947.3 22474 22503 SARS-CoV-2_74_RIGHT_1 2 - +MN908947.3 22402 22428 SARS-CoV-2_75_LEFT_1 1 + +MN908947.3 22785 22805 SARS-CoV-2_75_RIGHT_1 1 - +MN908947.3 22648 22677 SARS-CoV-2_76_LEFT_2 2 + +MN908947.3 22742 22774 SARS-CoV-2_76_LEFT_1 2 + +MN908947.3 23028 23057 SARS-CoV-2_76_RIGHT_2 2 - +MN908947.3 23120 23141 SARS-CoV-2_76_RIGHT_1 2 - +MN908947.3 22944 22974 SARS-CoV-2_77_LEFT_1 1 + +MN908947.3 23327 23351 SARS-CoV-2_77_RIGHT_1 1 - +MN908947.3 23219 23246 SARS-CoV-2_78_LEFT_1 2 + +MN908947.3 23611 23635 SARS-CoV-2_78_RIGHT_1 2 - +MN908947.3 23553 23575 SARS-CoV-2_79_LEFT_1 1 + +MN908947.3 23914 23944 SARS-CoV-2_79_RIGHT_1 1 - +MN908947.3 23927 23955 SARS-CoV-2_79_RIGHT_2 1 - +MN908947.3 23853 23876 SARS-CoV-2_80_LEFT_1 2 + +MN908947.3 24233 24258 SARS-CoV-2_80_RIGHT_1 2 - +MN908947.3 24171 24194 SARS-CoV-2_81_LEFT_1 1 + +MN908947.3 24545 24567 SARS-CoV-2_81_RIGHT_1 1 - +MN908947.3 24426 24448 SARS-CoV-2_82_LEFT_1 2 + +MN908947.3 24814 24836 SARS-CoV-2_82_RIGHT_1 2 - +MN908947.3 24750 24772 SARS-CoV-2_83_LEFT_1 1 + +MN908947.3 25122 25150 SARS-CoV-2_83_RIGHT_1 1 - +MN908947.3 25051 25076 SARS-CoV-2_84_LEFT_1 2 + +MN908947.3 25438 25461 SARS-CoV-2_84_RIGHT_1 2 - +MN908947.3 25331 25353 SARS-CoV-2_85_LEFT_1 1 + +MN908947.3 25711 25740 SARS-CoV-2_85_RIGHT_1 1 - +MN908947.3 25645 25672 SARS-CoV-2_86_LEFT_1 2 + +MN908947.3 26026 26050 SARS-CoV-2_86_RIGHT_1 2 - +MN908947.3 25951 25979 SARS-CoV-2_87_LEFT_1 1 + +MN908947.3 26338 26360 SARS-CoV-2_87_RIGHT_1 1 - +MN908947.3 26242 26268 SARS-CoV-2_88_LEFT_2 2 + +MN908947.3 26255 26277 SARS-CoV-2_88_LEFT_1 2 + +MN908947.3 26635 26661 SARS-CoV-2_88_RIGHT_1 2 - +MN908947.3 26564 26587 SARS-CoV-2_89_LEFT_1 1 + +MN908947.3 26592 26621 SARS-CoV-2_89_LEFT_2 1 + +MN908947.3 26956 26979 SARS-CoV-2_89_RIGHT_1 1 - +MN908947.3 26966 26991 SARS-CoV-2_89_RIGHT_2 1 - +MN908947.3 26873 26895 SARS-CoV-2_90_LEFT_1 2 + +MN908947.3 27218 27251 SARS-CoV-2_90_RIGHT_1 2 - +MN908947.3 27256 27283 SARS-CoV-2_90_RIGHT_2 2 - +MN908947.3 27152 27177 SARS-CoV-2_91_LEFT_1 1 + +MN908947.3 27534 27560 SARS-CoV-2_91_RIGHT_1 1 - +MN908947.3 27447 27473 SARS-CoV-2_92_LEFT_1 2 + +MN908947.3 27826 27855 SARS-CoV-2_92_RIGHT_1 2 - +MN908947.3 27700 27726 SARS-CoV-2_93_LEFT_1 1 + +MN908947.3 28082 28104 SARS-CoV-2_93_RIGHT_1 1 - +MN908947.3 27996 28021 SARS-CoV-2_94_LEFT_1 2 + +MN908947.3 28394 28416 SARS-CoV-2_94_RIGHT_1 2 - +MN908947.3 28190 28214 SARS-CoV-2_95_LEFT_1 1 + +MN908947.3 28572 28598 SARS-CoV-2_95_RIGHT_1 1 - +MN908947.3 28512 28536 SARS-CoV-2_96_LEFT_1 2 + +MN908947.3 28893 28914 SARS-CoV-2_96_RIGHT_1 2 - +MN908947.3 28827 28849 SARS-CoV-2_97_LEFT_1 1 + +MN908947.3 29206 29227 SARS-CoV-2_97_RIGHT_1 1 - +MN908947.3 29136 29161 SARS-CoV-2_98_LEFT_1 2 + +MN908947.3 29512 29534 SARS-CoV-2_98_RIGHT_1 2 - +MN908947.3 29452 29475 SARS-CoV-2_99_LEFT_1 1 + +MN908947.3 29827 29854 SARS-CoV-2_99_RIGHT_1 1 - diff --git a/test/data/primer-schemes/schemes/sars-cov-2/eden/2500/v1.0.0/info.yml b/test/data/primer-schemes/schemes/sars-cov-2/eden/2500/v1.0.0/info.yml new file mode 100644 index 0000000..ee83b42 --- /dev/null +++ b/test/data/primer-schemes/schemes/sars-cov-2/eden/2500/v1.0.0/info.yml @@ -0,0 +1,18 @@ +schema_version: 1.0.0a +organism: sars-cov-2 +name: eden +amplicon_size: 2500 +version: v1.0.0 +aliases: +- sydney +developers: +- John-Sebastian Eden +- Eby Sim +definition_url: https://github.com/pha4ge/primer-schemes/blob/main/schemes/sars-cov-2/eden/2500/v1.0.0 +citations: +- https://dx.doi.org/10.17504/protocols.io.befyjbpw +notes: +- Protocol includes addendum for ONT sequencing +license: CC-BY-4.0 +primer_checksum: primaschema:55c9726eb1400cab +reference_checksum: primaschema:b1acd7163146bf17 diff --git a/test/data/primer-schemes/schemes/sars-cov-2/eden/2500/v1.0.0/primer.bed b/test/data/primer-schemes/schemes/sars-cov-2/eden/2500/v1.0.0/primer.bed new file mode 100644 index 0000000..8fee45a --- /dev/null +++ b/test/data/primer-schemes/schemes/sars-cov-2/eden/2500/v1.0.0/primer.bed @@ -0,0 +1,28 @@ +MN908947.3 31 55 SARS2_1_LEFT_1 1 + CCAACCAACTTTCGATCTCTTGTA +MN908947.3 2569 2593 SARS2_1_RIGHT_1 1 - AGCTTCAACAGCTTCACTAGTAGG +MN908947.3 1876 1898 SARS2_2_LEFT_1 2 + TCAGAGGCTGCTCGTGTTGTAC +MN908947.3 4429 4451 SARS2_2_RIGHT_1 2 - TAGTTTCCACACAGACAGGCAT +MN908947.3 4295 4322 SARS2_3_LEFT_1 1 + CAGTGCTTAAAAAGTGTAAAAGTGCCT +MN908947.3 6847 6874 SARS2_3_RIGHT_1 1 - AACAGTATTCTTTGCTATAGTAGTCGG +MN908947.3 6287 6311 SARS2_4_LEFT_1 2 + GGTGTATACGTTGTCTTTGGAGCA +MN908947.3 8828 8852 SARS2_4_RIGHT_1 2 - CCACTTCTCTTGTTATGACTGCAG +MN908947.3 8596 8620 SARS2_5_LEFT_1 1 + CTTGTGTTCCTTTTTGTTGCTGCT +MN908947.3 11049 11075 SARS2_5_RIGHT_1 1 - AGAACAAAGACCATTGAGTACTCTGG +MN908947.3 10363 10385 SARS2_6_LEFT_1 2 + GTTCGCATTCAACCAGGACAGA +MN908947.3 12780 12803 SARS2_6_RIGHT_1 2 - ACCTACCTCCCTTTGTTGTGTTG +MN908947.3 12711 12733 SARS2_7_LEFT_1 1 + ACGACAGATGTCTTGTGCTGCC +MN908947.3 15225 15247 SARS2_7_RIGHT_1 1 - TTAACATGTTGTGCCAACCACC +MN908947.3 14546 14571 SARS2_8_LEFT_1 2 + GGAATTACTTGTGTATGCTGCTGAC +MN908947.3 17131 17153 SARS2_8_RIGHT_1 2 - TACACTATGCGAGCAGAAGGGT +MN908947.3 16847 16872 SARS2_9_LEFT_1 1 + CTATGGTGATGCTGTTGTTTACCGA +MN908947.3 19254 19279 SARS2_9_RIGHT_1 1 - AACCAGGCAAGTTAAGGTTAGATAG +MN908947.3 18897 18919 SARS2_10_LEFT_1 2 + GTTAAGCGTGTTGACTGGACTA +MN908947.3 21428 21456 SARS2_10_RIGHT_1 2 - TTGACCTTCTTTTAAAGACATAACAGCA +MN908947.3 21358 21387 SARS2_11_LEFT_1 1 + CAAATCCAATTCAGTTGTCTTCCTATTCT +MN908947.3 23823 23848 SARS2_11_RIGHT_1 1 - TTGTGTACAAAAACTGCCATATTGC +MN908947.3 23123 23145 SARS2_12_LEFT_1 2 + CAGCAACTGTTTGTGGACCTAA +MN908947.3 25647 25674 SARS2_12_RIGHT_1 2 - AAGGTGTGAGTAAACTGTTACAAACAA +MN908947.3 25602 25624 SARS2_13_LEFT_1 1 + CTAGCACTCTCCAAGGGTGTTC +MN908947.3 28146 28173 SARS2_13_RIGHT_1 1 - TAGGTTCCTGGCAATTAATTGTAAAAG +MN908947.3 27447 27472 SARS2_14_LEFT_1 2 + CACTACCAAGAGTGTGTTAGAGGTA +MN908947.3 29837 29867 SARS2_14_RIGHT_1 2 - ATTCTCCTAAGAAGCTATTAAAATCACATG diff --git a/test/data/primer-schemes/schemes/sars-cov-2/eden/2500/v1.0.0/primer.svg b/test/data/primer-schemes/schemes/sars-cov-2/eden/2500/v1.0.0/primer.svg new file mode 100644 index 0000000..3d07d0e --- /dev/null +++ b/test/data/primer-schemes/schemes/sars-cov-2/eden/2500/v1.0.0/primer.svg @@ -0,0 +1 @@ +12pool02,0004,0006,0008,00010,00012,00014,00016,00018,00020,00022,00024,00026,00028,00030,000MN908947.3+-strand \ No newline at end of file diff --git a/test/data/primer-schemes/schemes/sars-cov-2/eden/2500/v1.0.0/reference.fasta b/test/data/primer-schemes/schemes/sars-cov-2/eden/2500/v1.0.0/reference.fasta new file mode 100644 index 0000000..e1cfd92 --- /dev/null +++ b/test/data/primer-schemes/schemes/sars-cov-2/eden/2500/v1.0.0/reference.fasta @@ -0,0 +1,429 @@ +>MN908947.3 +ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAA +CGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAAC +TAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTG +TTGCAGCCGATCATCAGCACATCTAGGTTTCGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTC +CCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTAC +GTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGG +CTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAAACGTTCGGAT +GCTCGAACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACTCGAAGGCATTCAGTACGGTC +GTAGTGGTGAGACACTTGGTGTCCTTGTCCCTCATGTGGGCGAAATACCAGTGGCTTACCGCAAGGTTCT +TCTTCGTAAGAACGGTAATAAAGGAGCTGGTGGCCATAGTTACGGCGCCGATCTAAAGTCATTTGACTTA +GGCGACGAGCTTGGCACTGATCCTTATGAAGATTTTCAAGAAAACTGGAACACTAAACATAGCAGTGGTG +TTACCCGTGAACTCATGCGTGAGCTTAACGGAGGGGCATACACTCGCTATGTCGATAACAACTTCTGTGG +CCCTGATGGCTACCCTCTTGAGTGCATTAAAGACCTTCTAGCACGTGCTGGTAAAGCTTCATGCACTTTG +TCCGAACAACTGGACTTTATTGACACTAAGAGGGGTGTATACTGCTGCCGTGAACATGAGCATGAAATTG +CTTGGTACACGGAACGTTCTGAAAAGAGCTATGAATTGCAGACACCTTTTGAAATTAAATTGGCAAAGAA +ATTTGACACCTTCAATGGGGAATGTCCAAATTTTGTATTTCCCTTAAATTCCATAATCAAGACTATTCAA +CCAAGGGTTGAAAAGAAAAAGCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCCAGTTGCGTCAC +CAAATGAATGCAACCAAATGTGCCTTTCAACTCTCATGAAGTGTGATCATTGTGGTGAAACTTCATGGCA +GACGGGCGATTTTGTTAAAGCCACTTGCGAATTTTGTGGCACTGAGAATTTGACTAAAGAAGGTGCCACT +ACTTGTGGTTACTTACCCCAAAATGCTGTTGTTAAAATTTATTGTCCAGCATGTCACAATTCAGAAGTAG +GACCTGAGCATAGTCTTGCCGAATACCATAATGAATCTGGCTTGAAAACCATTCTTCGTAAGGGTGGTCG +CACTATTGCCTTTGGAGGCTGTGTGTTCTCTTATGTTGGTTGCCATAACAAGTGTGCCTATTGGGTTCCA +CGTGCTAGCGCTAACATAGGTTGTAACCATACAGGTGTTGTTGGAGAAGGTTCCGAAGGTCTTAATGACA +ACCTTCTTGAAATACTCCAAAAAGAGAAAGTCAACATCAATATTGTTGGTGACTTTAAACTTAATGAAGA +GATCGCCATTATTTTGGCATCTTTTTCTGCTTCCACAAGTGCTTTTGTGGAAACTGTGAAAGGTTTGGAT +TATAAAGCATTCAAACAAATTGTTGAATCCTGTGGTAATTTTAAAGTTACAAAAGGAAAAGCTAAAAAAG +GTGCCTGGAATATTGGTGAACAGAAATCAATACTGAGTCCTCTTTATGCATTTGCATCAGAGGCTGCTCG +TGTTGTACGATCAATTTTCTCCCGCACTCTTGAAACTGCTCAAAATTCTGTGCGTGTTTTACAGAAGGCC +GCTATAACAATACTAGATGGAATTTCACAGTATTCACTGAGACTCATTGATGCTATGATGTTCACATCTG +ATTTGGCTACTAACAATCTAGTTGTAATGGCCTACATTACAGGTGGTGTTGTTCAGTTGACTTCGCAGTG +GCTAACTAACATCTTTGGCACTGTTTATGAAAAACTCAAACCCGTCCTTGATTGGCTTGAAGAGAAGTTT +AAGGAAGGTGTAGAGTTTCTTAGAGACGGTTGGGAAATTGTTAAATTTATCTCAACCTGTGCTTGTGAAA +TTGTCGGTGGACAAATTGTCACCTGTGCAAAGGAAATTAAGGAGAGTGTTCAGACATTCTTTAAGCTTGT +AAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGCCTTGAATTTA +GGTGAAACATTTGTCACGCACTCAAAGGGATTGTACAGAAAGTGTGTTAAATCCAGAGAAGAAACTGGCC +TACTCATGCCTCTAAAAGCCCCAAAAGAAATTATCTTCTTAGAGGGAGAAACACTTCCCACAGAAGTGTT +AACAGAGGAAGTTGTCTTGAAAACTGGTGATTTACAACCATTAGAACAACCTACTAGTGAAGCTGTTGAA +GCTCCATTGGTTGGTACACCAGTTTGTATTAACGGGCTTATGTTGCTCGAAATCAAAGACACAGAAAAGT +ACTGTGCCCTTGCACCTAATATGATGGTAACAAACAATACCTTCACACTCAAAGGCGGTGCACCAACAAA +GGTTACTTTTGGTGATGACACTGTGATAGAAGTGCAAGGTTACAAGAGTGTGAATATCACTTTTGAACTT +GATGAAAGGATTGATAAAGTACTTAATGAGAAGTGCTCTGCCTATACAGTTGAACTCGGTACAGAAGTAA +ATGAGTTCGCCTGTGTTGTGGCAGATGCTGTCATAAAAACTTTGCAACCAGTATCTGAATTACTTACACC +ACTGGGCATTGATTTAGATGAGTGGAGTATGGCTACATACTACTTATTTGATGAGTCTGGTGAGTTTAAA +TTGGCTTCACATATGTATTGTTCTTTCTACCCTCCAGATGAGGATGAAGAAGAAGGTGATTGTGAAGAAG +AAGAGTTTGAGCCATCAACTCAATATGAGTATGGTACTGAAGATGATTACCAAGGTAAACCTTTGGAATT +TGGTGCCACTTCTGCTGCTCTTCAACCTGAAGAAGAGCAAGAAGAAGATTGGTTAGATGATGATAGTCAA +CAAACTGTTGGTCAACAAGACGGCAGTGAGGACAATCAGACAACTACTATTCAAACAATTGTTGAGGTTC +AACCTCAATTAGAGATGGAACTTACACCAGTTGTTCAGACTATTGAAGTGAATAGTTTTAGTGGTTATTT +AAAACTTACTGACAATGTATACATTAAAAATGCAGACATTGTGGAAGAAGCTAAAAAGGTAAAACCAACA +GTGGTTGTTAATGCAGCCAATGTTTACCTTAAACATGGAGGAGGTGTTGCAGGAGCCTTAAATAAGGCTA +CTAACAATGCCATGCAAGTTGAATCTGATGATTACATAGCTACTAATGGACCACTTAAAGTGGGTGGTAG +TTGTGTTTTAAGCGGACACAATCTTGCTAAACACTGTCTTCATGTTGTCGGCCCAAATGTTAACAAAGGT +GAAGACATTCAACTTCTTAAGAGTGCTTATGAAAATTTTAATCAGCACGAAGTTCTACTTGCACCATTAT +TATCAGCTGGTATTTTTGGTGCTGACCCTATACATTCTTTAAGAGTTTGTGTAGATACTGTTCGCACAAA +TGTCTACTTAGCTGTCTTTGATAAAAATCTCTATGACAAACTTGTTTCAAGCTTTTTGGAAATGAAGAGT +GAAAAGCAAGTTGAACAAAAGATCGCTGAGATTCCTAAAGAGGAAGTTAAGCCATTTATAACTGAAAGTA +AACCTTCAGTTGAACAGAGAAAACAAGATGATAAGAAAATCAAAGCTTGTGTTGAAGAAGTTACAACAAC +TCTGGAAGAAACTAAGTTCCTCACAGAAAACTTGTTACTTTATATTGACATTAATGGCAATCTTCATCCA +GATTCTGCCACTCTTGTTAGTGACATTGACATCACTTTCTTAAAGAAAGATGCTCCATATATAGTGGGTG +ATGTTGTTCAAGAGGGTGTTTTAACTGCTGTGGTTATACCTACTAAAAAGGCTGGTGGCACTACTGAAAT +GCTAGCGAAAGCTTTGAGAAAAGTGCCAACAGACAATTATATAACCACTTACCCGGGTCAGGGTTTAAAT +GGTTACACTGTAGAGGAGGCAAAGACAGTGCTTAAAAAGTGTAAAAGTGCCTTTTACATTCTACCATCTA +TTATCTCTAATGAGAAGCAAGAAATTCTTGGAACTGTTTCTTGGAATTTGCGAGAAATGCTTGCACATGC +AGAAGAAACACGCAAATTAATGCCTGTCTGTGTGGAAACTAAAGCCATAGTTTCAACTATACAGCGTAAA +TATAAGGGTATTAAAATACAAGAGGGTGTGGTTGATTATGGTGCTAGATTTTACTTTTACACCAGTAAAA +CAACTGTAGCGTCACTTATCAACACACTTAACGATCTAAATGAAACTCTTGTTACAATGCCACTTGGCTA +TGTAACACATGGCTTAAATTTGGAAGAAGCTGCTCGGTATATGAGATCTCTCAAAGTGCCAGCTACAGTT +TCTGTTTCTTCACCTGATGCTGTTACAGCGTATAATGGTTATCTTACTTCTTCTTCTAAAACACCTGAAG +AACATTTTATTGAAACCATCTCACTTGCTGGTTCCTATAAAGATTGGTCCTATTCTGGACAATCTACACA +ACTAGGTATAGAATTTCTTAAGAGAGGTGATAAAAGTGTATATTACACTAGTAATCCTACCACATTCCAC +CTAGATGGTGAAGTTATCACCTTTGACAATCTTAAGACACTTCTTTCTTTGAGAGAAGTGAGGACTATTA +AGGTGTTTACAACAGTAGACAACATTAACCTCCACACGCAAGTTGTGGACATGTCAATGACATATGGACA +ACAGTTTGGTCCAACTTATTTGGATGGAGCTGATGTTACTAAAATAAAACCTCATAATTCACATGAAGGT +AAAACATTTTATGTTTTACCTAATGATGACACTCTACGTGTTGAGGCTTTTGAGTACTACCACACAACTG +ATCCTAGTTTTCTGGGTAGGTACATGTCAGCATTAAATCACACTAAAAAGTGGAAATACCCACAAGTTAA +TGGTTTAACTTCTATTAAATGGGCAGATAACAACTGTTATCTTGCCACTGCATTGTTAACACTCCAACAA +ATAGAGTTGAAGTTTAATCCACCTGCTCTACAAGATGCTTATTACAGAGCAAGGGCTGGTGAAGCTGCTA +ACTTTTGTGCACTTATCTTAGCCTACTGTAATAAGACAGTAGGTGAGTTAGGTGATGTTAGAGAAACAAT +GAGTTACTTGTTTCAACATGCCAATTTAGATTCTTGCAAAAGAGTCTTGAACGTGGTGTGTAAAACTTGT +GGACAACAGCAGACAACCCTTAAGGGTGTAGAAGCTGTTATGTACATGGGCACACTTTCTTATGAACAAT +TTAAGAAAGGTGTTCAGATACCTTGTACGTGTGGTAAACAAGCTACAAAATATCTAGTACAACAGGAGTC +ACCTTTTGTTATGATGTCAGCACCACCTGCTCAGTATGAACTTAAGCATGGTACATTTACTTGTGCTAGT +GAGTACACTGGTAATTACCAGTGTGGTCACTATAAACATATAACTTCTAAAGAAACTTTGTATTGCATAG +ACGGTGCTTTACTTACAAAGTCCTCAGAATACAAAGGTCCTATTACGGATGTTTTCTACAAAGAAAACAG +TTACACAACAACCATAAAACCAGTTACTTATAAATTGGATGGTGTTGTTTGTACAGAAATTGACCCTAAG +TTGGACAATTATTATAAGAAAGACAATTCTTATTTCACAGAGCAACCAATTGATCTTGTACCAAACCAAC +CATATCCAAACGCAAGCTTCGATAATTTTAAGTTTGTATGTGATAATATCAAATTTGCTGATGATTTAAA +CCAGTTAACTGGTTATAAGAAACCTGCTTCAAGAGAGCTTAAAGTTACATTTTTCCCTGACTTAAATGGT +GATGTGGTGGCTATTGATTATAAACACTACACACCCTCTTTTAAGAAAGGAGCTAAATTGTTACATAAAC +CTATTGTTTGGCATGTTAACAATGCAACTAATAAAGCCACGTATAAACCAAATACCTGGTGTATACGTTG +TCTTTGGAGCACAAAACCAGTTGAAACATCAAATTCGTTTGATGTACTGAAGTCAGAGGACGCGCAGGGA +ATGGATAATCTTGCCTGCGAAGATCTAAAACCAGTCTCTGAAGAAGTAGTGGAAAATCCTACCATACAGA +AAGACGTTCTTGAGTGTAATGTGAAAACTACCGAAGTTGTAGGAGACATTATACTTAAACCAGCAAATAA +TAGTTTAAAAATTACAGAAGAGGTTGGCCACACAGATCTAATGGCTGCTTATGTAGACAATTCTAGTCTT +ACTATTAAGAAACCTAATGAATTATCTAGAGTATTAGGTTTGAAAACCCTTGCTACTCATGGTTTAGCTG +CTGTTAATAGTGTCCCTTGGGATACTATAGCTAATTATGCTAAGCCTTTTCTTAACAAAGTTGTTAGTAC +AACTACTAACATAGTTACACGGTGTTTAAACCGTGTTTGTACTAATTATATGCCTTATTTCTTTACTTTA +TTGCTACAATTGTGTACTTTTACTAGAAGTACAAATTCTAGAATTAAAGCATCTATGCCGACTACTATAG +CAAAGAATACTGTTAAGAGTGTCGGTAAATTTTGTCTAGAGGCTTCATTTAATTATTTGAAGTCACCTAA +TTTTTCTAAACTGATAAATATTATAATTTGGTTTTTACTATTAAGTGTTTGCCTAGGTTCTTTAATCTAC +TCAACCGCTGCTTTAGGTGTTTTAATGTCTAATTTAGGCATGCCTTCTTACTGTACTGGTTACAGAGAAG +GCTATTTGAACTCTACTAATGTCACTATTGCAACCTACTGTACTGGTTCTATACCTTGTAGTGTTTGTCT +TAGTGGTTTAGATTCTTTAGACACCTATCCTTCTTTAGAAACTATACAAATTACCATTTCATCTTTTAAA +TGGGATTTAACTGCTTTTGGCTTAGTTGCAGAGTGGTTTTTGGCATATATTCTTTTCACTAGGTTTTTCT +ATGTACTTGGATTGGCTGCAATCATGCAATTGTTTTTCAGCTATTTTGCAGTACATTTTATTAGTAATTC +TTGGCTTATGTGGTTAATAATTAATCTTGTACAAATGGCCCCGATTTCAGCTATGGTTAGAATGTACATC +TTCTTTGCATCATTTTATTATGTATGGAAAAGTTATGTGCATGTTGTAGACGGTTGTAATTCATCAACTT +GTATGATGTGTTACAAACGTAATAGAGCAACAAGAGTCGAATGTACAACTATTGTTAATGGTGTTAGAAG +GTCCTTTTATGTCTATGCTAATGGAGGTAAAGGCTTTTGCAAACTACACAATTGGAATTGTGTTAATTGT +GATACATTCTGTGCTGGTAGTACATTTATTAGTGATGAAGTTGCGAGAGACTTGTCACTACAGTTTAAAA +GACCAATAAATCCTACTGACCAGTCTTCTTACATCGTTGATAGTGTTACAGTGAAGAATGGTTCCATCCA +TCTTTACTTTGATAAAGCTGGTCAAAAGACTTATGAAAGACATTCTCTCTCTCATTTTGTTAACTTAGAC +AACCTGAGAGCTAATAACACTAAAGGTTCATTGCCTATTAATGTTATAGTTTTTGATGGTAAATCAAAAT +GTGAAGAATCATCTGCAAAATCAGCGTCTGTTTACTACAGTCAGCTTATGTGTCAACCTATACTGTTACT +AGATCAGGCATTAGTGTCTGATGTTGGTGATAGTGCGGAAGTTGCAGTTAAAATGTTTGATGCTTACGTT +AATACGTTTTCATCAACTTTTAACGTACCAATGGAAAAACTCAAAACACTAGTTGCAACTGCAGAAGCTG +AACTTGCAAAGAATGTGTCCTTAGACAATGTCTTATCTACTTTTATTTCAGCAGCTCGGCAAGGGTTTGT +TGATTCAGATGTAGAAACTAAAGATGTTGTTGAATGTCTTAAATTGTCACATCAATCTGACATAGAAGTT +ACTGGCGATAGTTGTAATAACTATATGCTCACCTATAACAAAGTTGAAAACATGACACCCCGTGACCTTG +GTGCTTGTATTGACTGTAGTGCGCGTCATATTAATGCGCAGGTAGCAAAAAGTCACAACATTGCTTTGAT +ATGGAACGTTAAAGATTTCATGTCATTGTCTGAACAACTACGAAAACAAATACGTAGTGCTGCTAAAAAG +AATAACTTACCTTTTAAGTTGACATGTGCAACTACTAGACAAGTTGTTAATGTTGTAACAACAAAGATAG +CACTTAAGGGTGGTAAAATTGTTAATAATTGGTTGAAGCAGTTAATTAAAGTTACACTTGTGTTCCTTTT +TGTTGCTGCTATTTTCTATTTAATAACACCTGTTCATGTCATGTCTAAACATACTGACTTTTCAAGTGAA +ATCATAGGATACAAGGCTATTGATGGTGGTGTCACTCGTGACATAGCATCTACAGATACTTGTTTTGCTA +ACAAACATGCTGATTTTGACACATGGTTTAGCCAGCGTGGTGGTAGTTATACTAATGACAAAGCTTGCCC +ATTGATTGCTGCAGTCATAACAAGAGAAGTGGGTTTTGTCGTGCCTGGTTTGCCTGGCACGATATTACGC +ACAACTAATGGTGACTTTTTGCATTTCTTACCTAGAGTTTTTAGTGCAGTTGGTAACATCTGTTACACAC +CATCAAAACTTATAGAGTACACTGACTTTGCAACATCAGCTTGTGTTTTGGCTGCTGAATGTACAATTTT +TAAAGATGCTTCTGGTAAGCCAGTACCATATTGTTATGATACCAATGTACTAGAAGGTTCTGTTGCTTAT +GAAAGTTTACGCCCTGACACACGTTATGTGCTCATGGATGGCTCTATTATTCAATTTCCTAACACCTACC +TTGAAGGTTCTGTTAGAGTGGTAACAACTTTTGATTCTGAGTACTGTAGGCACGGCACTTGTGAAAGATC +AGAAGCTGGTGTTTGTGTATCTACTAGTGGTAGATGGGTACTTAACAATGATTATTACAGATCTTTACCA +GGAGTTTTCTGTGGTGTAGATGCTGTAAATTTACTTACTAATATGTTTACACCACTAATTCAACCTATTG +GTGCTTTGGACATATCAGCATCTATAGTAGCTGGTGGTATTGTAGCTATCGTAGTAACATGCCTTGCCTA +CTATTTTATGAGGTTTAGAAGAGCTTTTGGTGAATACAGTCATGTAGTTGCCTTTAATACTTTACTATTC +CTTATGTCATTCACTGTACTCTGTTTAACACCAGTTTACTCATTCTTACCTGGTGTTTATTCTGTTATTT +ACTTGTACTTGACATTTTATCTTACTAATGATGTTTCTTTTTTAGCACATATTCAGTGGATGGTTATGTT +CACACCTTTAGTACCTTTCTGGATAACAATTGCTTATATCATTTGTATTTCCACAAAGCATTTCTATTGG +TTCTTTAGTAATTACCTAAAGAGACGTGTAGTCTTTAATGGTGTTTCCTTTAGTACTTTTGAAGAAGCTG +CGCTGTGCACCTTTTTGTTAAATAAAGAAATGTATCTAAAGTTGCGTAGTGATGTGCTATTACCTCTTAC +GCAATATAATAGATACTTAGCTCTTTATAATAAGTACAAGTATTTTAGTGGAGCAATGGATACAACTAGC +TACAGAGAAGCTGCTTGTTGTCATCTCGCAAAGGCTCTCAATGACTTCAGTAACTCAGGTTCTGATGTTC +TTTACCAACCACCACAAACCTCTATCACCTCAGCTGTTTTGCAGAGTGGTTTTAGAAAAATGGCATTCCC +ATCTGGTAAAGTTGAGGGTTGTATGGTACAAGTAACTTGTGGTACAACTACACTTAACGGTCTTTGGCTT +GATGACGTAGTTTACTGTCCAAGACATGTGATCTGCACCTCTGAAGACATGCTTAACCCTAATTATGAAG +ATTTACTCATTCGTAAGTCTAATCATAATTTCTTGGTACAGGCTGGTAATGTTCAACTCAGGGTTATTGG +ACATTCTATGCAAAATTGTGTACTTAAGCTTAAGGTTGATACAGCCAATCCTAAGACACCTAAGTATAAG +TTTGTTCGCATTCAACCAGGACAGACTTTTTCAGTGTTAGCTTGTTACAATGGTTCACCATCTGGTGTTT +ACCAATGTGCTATGAGGCCCAATTTCACTATTAAGGGTTCATTCCTTAATGGTTCATGTGGTAGTGTTGG +TTTTAACATAGATTATGACTGTGTCTCTTTTTGTTACATGCACCATATGGAATTACCAACTGGAGTTCAT +GCTGGCACAGACTTAGAAGGTAACTTTTATGGACCTTTTGTTGACAGGCAAACAGCACAAGCAGCTGGTA +CGGACACAACTATTACAGTTAATGTTTTAGCTTGGTTGTACGCTGCTGTTATAAATGGAGACAGGTGGTT +TCTCAATCGATTTACCACAACTCTTAATGACTTTAACCTTGTGGCTATGAAGTACAATTATGAACCTCTA +ACACAAGACCATGTTGACATACTAGGACCTCTTTCTGCTCAAACTGGAATTGCCGTTTTAGATATGTGTG +CTTCATTAAAAGAATTACTGCAAAATGGTATGAATGGACGTACCATATTGGGTAGTGCTTTATTAGAAGA +TGAATTTACACCTTTTGATGTTGTTAGACAATGCTCAGGTGTTACTTTCCAAAGTGCAGTGAAAAGAACA +ATCAAGGGTACACACCACTGGTTGTTACTCACAATTTTGACTTCACTTTTAGTTTTAGTCCAGAGTACTC +AATGGTCTTTGTTCTTTTTTTTGTATGAAAATGCCTTTTTACCTTTTGCTATGGGTATTATTGCTATGTC +TGCTTTTGCAATGATGTTTGTCAAACATAAGCATGCATTTCTCTGTTTGTTTTTGTTACCTTCTCTTGCC +ACTGTAGCTTATTTTAATATGGTCTATATGCCTGCTAGTTGGGTGATGCGTATTATGACATGGTTGGATA +TGGTTGATACTAGTTTGTCTGGTTTTAAGCTAAAAGACTGTGTTATGTATGCATCAGCTGTAGTGTTACT +AATCCTTATGACAGCAAGAACTGTGTATGATGATGGTGCTAGGAGAGTGTGGACACTTATGAATGTCTTG +ACACTCGTTTATAAAGTTTATTATGGTAATGCTTTAGATCAAGCCATTTCCATGTGGGCTCTTATAATCT +CTGTTACTTCTAACTACTCAGGTGTAGTTACAACTGTCATGTTTTTGGCCAGAGGTATTGTTTTTATGTG +TGTTGAGTATTGCCCTATTTTCTTCATAACTGGTAATACACTTCAGTGTATAATGCTAGTTTATTGTTTC +TTAGGCTATTTTTGTACTTGTTACTTTGGCCTCTTTTGTTTACTCAACCGCTACTTTAGACTGACTCTTG +GTGTTTATGATTACTTAGTTTCTACACAGGAGTTTAGATATATGAATTCACAGGGACTACTCCCACCCAA +GAATAGCATAGATGCCTTCAAACTCAACATTAAATTGTTGGGTGTTGGTGGCAAACCTTGTATCAAAGTA +GCCACTGTACAGTCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAAC +TCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAA +AGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTA +GACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAAGCTATAGCCTCAGAGTTTA +GTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGA +TTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCA +GCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTG +AGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAA +TGATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACA +ACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACAT +TTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAG +TGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCT +GCTGTCAAATTACAGAATAATGAGCTTAGTCCTGTTGCACTACGACAGATGTCTTGTGCTGCCGGTACTA +CACAAACTGCTTGCACTGATGACAATGCGTTAGCTTACTACAACACAACAAAGGGAGGTAGGTTTGTACT +TGCACTGTTATCCGATTTACAGGATTTGAAATGGGCTAGATTCCCTAAGAGTGATGGAACTGGTACTATC +TATACAGAACTGGAACCACCTTGTAGGTTTGTTACAGACACACCTAAAGGTCCTAAAGTGAAGTATTTAT +ACTTTATTAAAGGATTAAACAACCTAAATAGAGGTATGGTACTTGGTAGTTTAGCTGCCACAGTACGTCT +ACAAGCTGGTAATGCAACAGAAGTGCCTGCCAATTCAACTGTATTATCTTTCTGTGCTTTTGCTGTAGAT +GCTGCTAAAGCTTACAAAGATTATCTAGCTAGTGGGGGACAACCAATCACTAATTGTGTTAAGATGTTGT +GTACACACACTGGTACTGGTCAGGCAATAACAGTTACACCGGAAGCCAATATGGATCAAGAATCCTTTGG +TGGTGCATCGTGTTGTCTGTACTGCCGTTGCCACATAGATCATCCAAATCCTAAAGGATTTTGTGACTTA +AAAGGTAAGTATGTACAAATACCTACAACTTGTGCTAATGACCCTGTGGGTTTTACACTTAAAAACACAG +TCTGTACCGTCTGCGGTATGTGGAAAGGTTATGGCTGTAGTTGTGATCAACTCCGCGAACCCATGCTTCA +GTCAGCTGATGCACAATCGTTTTTAAACGGGTTTGCGGTGTAAGTGCAGCCCGTCTTACACCGTGCGGCA +CAGGCACTAGTACTGATGTCGTATACAGGGCTTTTGACATCTACAATGATAAAGTAGCTGGTTTTGCTAA +ATTCCTAAAAACTAATTGTTGTCGCTTCCAAGAAAAGGACGAAGATGACAATTTAATTGATTCTTACTTT +GTAGTTAAGAGACACACTTTCTCTAACTACCAACATGAAGAAACAATTTATAATTTACTTAAGGATTGTC +CAGCTGTTGCTAAACATGACTTCTTTAAGTTTAGAATAGACGGTGACATGGTACCACATATATCACGTCA +ACGTCTTACTAAATACACAATGGCAGACCTCGTCTATGCTTTAAGGCATTTTGATGAAGGTAATTGTGAC +ACATTAAAAGAAATACTTGTCACATACAATTGTTGTGATGATGATTATTTCAATAAAAAGGACTGGTATG +ATTTTGTAGAAAACCCAGATATATTACGCGTATACGCCAACTTAGGTGAACGTGTACGCCAAGCTTTGTT +AAAAACAGTACAATTCTGTGATGCCATGCGAAATGCTGGTATTGTTGGTGTACTGACATTAGATAATCAA +GATCTCAATGGTAACTGGTATGATTTCGGTGATTTCATACAAACCACGCCAGGTAGTGGAGTTCCTGTTG +TAGATTCTTATTATTCATTGTTAATGCCTATATTAACCTTGACCAGGGCTTTAACTGCAGAGTCACATGT +TGACACTGACTTAACAAAGCCTTACATTAAGTGGGATTTGTTAAAATATGACTTCACGGAAGAGAGGTTA +AAACTCTTTGACCGTTATTTTAAATATTGGGATCAGACATACCACCCAAATTGTGTTAACTGTTTGGATG +ACAGATGCATTCTGCATTGTGCAAACTTTAATGTTTTATTCTCTACAGTGTTCCCACCTACAAGTTTTGG +ACCACTAGTGAGAAAAATATTTGTTGATGGTGTTCCATTTGTAGTTTCAACTGGATACCACTTCAGAGAG +CTAGGTGTTGTACATAATCAGGATGTAAACTTACATAGCTCTAGACTTAGTTTTAAGGAATTACTTGTGT +ATGCTGCTGACCCTGCTATGCACGCTGCTTCTGGTAATCTATTACTAGATAAACGCACTACGTGCTTTTC +AGTAGCTGCACTTACTAACAATGTTGCTTTTCAAACTGTCAAACCCGGTAATTTTAACAAAGACTTCTAT +GACTTTGCTGTGTCTAAGGGTTTCTTTAAGGAAGGAAGTTCTGTTGAATTAAAACACTTCTTCTTTGCTC +AGGATGGTAATGCTGCTATCAGCGATTATGACTACTATCGTTATAATCTACCAACAATGTGTGATATCAG +ACAACTACTATTTGTAGTTGAAGTTGTTGATAAGTACTTTGATTGTTACGATGGTGGCTGTATTAATGCT +AACCAAGTCATCGTCAACAACCTAGACAAATCAGCTGGTTTTCCATTTAATAAATGGGGTAAGGCTAGAC +TTTATTATGATTCAATGAGTTATGAGGATCAAGATGCACTTTTCGCATATACAAAACGTAATGTCATCCC +TACTATAACTCAAATGAATCTTAAGTATGCCATTAGTGCAAAGAATAGAGCTCGCACCGTAGCTGGTGTC +TCTATCTGTAGTACTATGACCAATAGACAGTTTCATCAAAAATTATTGAAATCAATAGCCGCCACTAGAG +GAGCTACTGTAGTAATTGGAACAAGCAAATTCTATGGTGGTTGGCACAACATGTTAAAAACTGTTTATAG +TGATGTAGAAAACCCTCACCTTATGGGTTGGGATTATCCTAAATGTGATAGAGCCATGCCTAACATGCTT +AGAATTATGGCCTCACTTGTTCTTGCTCGCAAACATACAACGTGTTGTAGCTTGTCACACCGTTTCTATA +GATTAGCTAATGAGTGTGCTCAAGTATTGAGTGAAATGGTCATGTGTGGCGGTTCACTATATGTTAAACC +AGGTGGAACCTCATCAGGAGATGCCACAACTGCTTATGCTAATAGTGTTTTTAACATTTGTCAAGCTGTC +ACGGCCAATGTTAATGCACTTTTATCTACTGATGGTAACAAAATTGCCGATAAGTATGTCCGCAATTTAC +AACACAGACTTTATGAGTGTCTCTATAGAAATAGAGATGTTGACACAGACTTTGTGAATGAGTTTTACGC +ATATTTGCGTAAACATTTCTCAATGATGATACTCTCTGACGATGCTGTTGTGTGTTTCAATAGCACTTAT +GCATCTCAAGGTCTAGTGGCTAGCATAAAGAACTTTAAGTCAGTTCTTTATTATCAAAACAATGTTTTTA +TGTCTGAAGCAAAATGTTGGACTGAGACTGACCTTACTAAAGGACCTCATGAATTTTGCTCTCAACATAC +AATGCTAGTTAAACAGGGTGATGATTATGTGTACCTTCCTTACCCAGATCCATCAAGAATCCTAGGGGCC +GGCTGTTTTGTAGATGATATCGTAAAAACAGATGGTACACTTATGATTGAACGGTTCGTGTCTTTAGCTA +TAGATGCTTACCCACTTACTAAACATCCTAATCAGGAGTATGCTGATGTCTTTCATTTGTACTTACAATA +CATAAGAAAGCTACATGATGAGTTAACAGGACACATGTTAGACATGTATTCTGTTATGCTTACTAATGAT +AACACTTCAAGGTATTGGGAACCTGAGTTTTATGAGGCTATGTACACACCGCATACAGTCTTACAGGCTG +TTGGGGCTTGTGTTCTTTGCAATTCACAGACTTCATTAAGATGTGGTGCTTGCATACGTAGACCATTCTT +ATGTTGTAAATGCTGTTACGACCATGTCATATCAACATCACATAAATTAGTCTTGTCTGTTAATCCGTAT +GTTTGCAATGCTCCAGGTTGTGATGTCACAGATGTGACTCAACTTTACTTAGGAGGTATGAGCTATTATT +GTAAATCACATAAACCACCCATTAGTTTTCCATTGTGTGCTAATGGACAAGTTTTTGGTTTATATAAAAA +TACATGTGTTGGTAGCGATAATGTTACTGACTTTAATGCAATTGCAACATGTGACTGGACAAATGCTGGT +GATTACATTTTAGCTAACACCTGTACTGAAAGACTCAAGCTTTTTGCAGCAGAAACGCTCAAAGCTACTG +AGGAGACATTTAAACTGTCTTATGGTATTGCTACTGTACGTGAAGTGCTGTCTGACAGAGAATTACATCT +TTCATGGGAAGTTGGTAAACCTAGACCACCACTTAACCGAAATTATGTCTTTACTGGTTATCGTGTAACT +AAAAACAGTAAAGTACAAATAGGAGAGTACACCTTTGAAAAAGGTGACTATGGTGATGCTGTTGTTTACC +GAGGTACAACAACTTACAAATTAAATGTTGGTGATTATTTTGTGCTGACATCACATACAGTAATGCCATT +AAGTGCACCTACACTAGTGCCACAAGAGCACTATGTTAGAATTACTGGCTTATACCCAACACTCAATATC +TCAGATGAGTTTTCTAGCAATGTTGCAAATTATCAAAAGGTTGGTATGCAAAAGTATTCTACACTCCAGG +GACCACCTGGTACTGGTAAGAGTCATTTTGCTATTGGCCTAGCTCTCTACTACCCTTCTGCTCGCATAGT +GTATACAGCTTGCTCTCATGCCGCTGTTGATGCACTATGTGAGAAGGCATTAAAATATTTGCCTATAGAT +AAATGTAGTAGAATTATACCTGCACGTGCTCGTGTAGAGTGTTTTGATAAATTCAAAGTGAATTCAACAT +TAGAACAGTATGTCTTTTGTACTGTAAATGCATTGCCTGAGACGACAGCAGATATAGTTGTCTTTGATGA +AATTTCAATGGCCACAAATTATGATTTGAGTGTTGTCAATGCCAGATTACGTGCTAAGCACTATGTGTAC +ATTGGCGACCCTGCTCAATTACCTGCACCACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATT +TCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCC +TGCTGAAATTGTTGACACTGTGAGTGCTTTGGTTTATGATAATAAGCTTAAAGCACATAAAGACAAATCA +GCTCAATGCTTTAAAATGTTTTATAAGGGTGTTATCACGCATGATGTTTCATCTGCAATTAACAGGCCAC +AAATAGGCGTGGTAAGAGAATTCCTTACACGTAACCCTGCTTGGAGAAAAGCTGTCTTTATTTCACCTTA +TAATTCACAGAATGCTGTAGCCTCAAAGATTTTGGGACTACCAACTCAAACTGTTGATTCATCACAGGGC +TCAGAATATGACTATGTCATATTCACTCAAACCACTGAAACAGCTCACTCTTGTAATGTAAACAGATTTA +ATGTTGCTATTACCAGAGCAAAAGTAGGCATACTTTGCATAATGTCTGATAGAGACCTTTATGACAAGTT +GCAATTTACAAGTCTTGAAATTCCACGTAGGAATGTGGCAACTTTACAAGCTGAAAATGTAACAGGACTC +TTTAAAGATTGTAGTAAGGTAATCACTGGGTTACATCCTACACAGGCACCTACACACCTCAGTGTTGACA +CTAAATTCAAAACTGAAGGTTTATGTGTTGACATACCTGGCATACCTAAGGACATGACCTATAGAAGACT +CATCTCTATGATGGGTTTTAAAATGAATTATCAAGTTAATGGTTACCCTAACATGTTTATCACCCGCGAA +GAAGCTATAAGACATGTACGTGCATGGATTGGCTTCGATGTCGAGGGGTGTCATGCTACTAGAGAAGCTG +TTGGTACCAATTTACCTTTACAGCTAGGTTTTTCTACAGGTGTTAACCTAGTTGCTGTACCTACAGGTTA +TGTTGATACACCTAATAATACAGATTTTTCCAGAGTTAGTGCTAAACCACCGCCTGGAGATCAATTTAAA +CACCTCATACCACTTATGTACAAAGGACTTCCTTGGAATGTAGTGCGTATAAAGATTGTACAAATGTTAA +GTGACACACTTAAAAATCTCTCTGACAGAGTCGTATTTGTCTTATGGGCACATGGCTTTGAGTTGACATC +TATGAAGTATTTTGTGAAAATAGGACCTGAGCGCACCTGTTGTCTATGTGATAGACGTGCCACATGCTTT +TCCACTGCTTCAGACACTTATGCCTGTTGGCATCATTCTATTGGATTTGATTACGTCTATAATCCGTTTA +TGATTGATGTTCAACAATGGGGTTTTACAGGTAACCTACAAAGCAACCATGATCTGTATTGTCAAGTCCA +TGGTAATGCACATGTAGCTAGTTGTGATGCAATCATGACTAGGTGTCTAGCTGTCCACGAGTGCTTTGTT +AAGCGTGTTGACTGGACTATTGAATATCCTATAATTGGTGATGAACTGAAGATTAATGCGGCTTGTAGAA +AGGTTCAACACATGGTTGTTAAAGCTGCATTATTAGCAGACAAATTCCCAGTTCTTCACGACATTGGTAA +CCCTAAAGCTATTAAGTGTGTACCTCAAGCTGATGTAGAATGGAAGTTCTATGATGCACAGCCTTGTAGT +GACAAAGCTTATAAAATAGAAGAATTATTCTATTCTTATGCCACACATTCTGACAAATTCACAGATGGTG +TATGCCTATTTTGGAATTGCAATGTCGATAGATATCCTGCTAATTCCATTGTTTGTAGATTTGACACTAG +AGTGCTATCTAACCTTAACTTGCCTGGTTGTGATGGTGGCAGTTTGTATGTAAATAAACATGCATTCCAC +ACACCAGCTTTTGATAAAAGTGCTTTTGTTAATTTAAAACAATTACCATTTTTCTATTACTCTGACAGTC +CATGTGAGTCTCATGGAAAACAAGTAGTGTCAGATATAGATTATGTACCACTAAAGTCTGCTACGTGTAT +AACACGTTGCAATTTAGGTGGTGCTGTCTGTAGACATCATGCTAATGAGTACAGATTGTATCTCGATGCT +TATAACATGATGATCTCAGCTGGCTTTAGCTTGTGGGTTTACAAACAATTTGATACTTATAACCTCTGGA +ACACTTTTACAAGACTTCAGAGTTTAGAAAATGTGGCTTTTAATGTTGTAAATAAGGGACACTTTGATGG +ACAACAGGGTGAAGTACCAGTTTCTATCATTAATAACACTGTTTACACAAAAGTTGATGGTGTTGATGTA +GAATTGTTTGAAAATAAAACAACATTACCTGTTAATGTAGCATTTGAGCTTTGGGCTAAGCGCAACATTA +AACCAGTACCAGAGGTGAAAATACTCAATAATTTGGGTGTGGACATTGCTGCTAATACTGTGATCTGGGA +CTACAAAAGAGATGCTCCAGCACATATATCTACTATTGGTGTTTGTTCTATGACTGACATAGCCAAGAAA +CCAACTGAAACGATTTGTGCACCACTCACTGTCTTTTTTGATGGTAGAGTTGATGGTCAAGTAGACTTAT +TTAGAAATGCCCGTAATGGTGTTCTTATTACAGAAGGTAGTGTTAAAGGTTTACAACCATCTGTAGGTCC +CAAACAAGCTAGTCTTAATGGAGTCACATTAATTGGAGAAGCCGTAAAAACACAGTTCAATTATTATAAG +AAAGTTGATGGTGTTGTCCAACAATTACCTGAAACTTACTTTACTCAGAGTAGAAATTTACAAGAATTTA +AACCCAGGAGTCAAATGGAAATTGATTTCTTAGAATTAGCTATGGATGAATTCATTGAACGGTATAAATT +AGAAGGCTATGCCTTCGAACATATCGTTTATGGAGATTTTAGTCATAGTCAGTTAGGTGGTTTACATCTA +CTGATTGGACTAGCTAAACGTTTTAAGGAATCACCTTTTGAATTAGAAGATTTTATTCCTATGGACAGTA +CAGTTAAAAACTATTTCATAACAGATGCGCAAACAGGTTCATCTAAGTGTGTGTGTTCTGTTATTGATTT +ATTACTTGATGATTTTGTTGAAATAATAAAATCCCAAGATTTATCTGTAGTTTCTAAGGTTGTCAAAGTG +ACTATTGACTATACAGAAATTTCATTTATGCTTTGGTGTAAAGATGGCCATGTAGAAACATTTTACCCAA +AATTACAATCTAGTCAAGCGTGGCAACCGGGTGTTGCTATGCCTAATCTTTACAAAATGCAAAGAATGCT +ATTAGAAAAGTGTGACCTTCAAAATTATGGTGATAGTGCAACATTACCTAAAGGCATAATGATGAATGTC +GCAAAATATACTCAACTGTGTCAATATTTAAACACATTAACATTAGCTGTACCCTATAATATGAGAGTTA +TACATTTTGGTGCTGGTTCTGATAAAGGAGTTGCACCAGGTACAGCTGTTTTAAGACAGTGGTTGCCTAC +GGGTACGCTGCTTGTCGATTCAGATCTTAATGACTTTGTCTCTGATGCAGATTCAACTTTGATTGGTGAT +TGTGCAACTGTACATACAGCTAATAAATGGGATCTCATTATTAGTGATATGTACGACCCTAAGACTAAAA +ATGTTACAAAAGAAAATGACTCTAAAGAGGGTTTTTTCACTTACATTTGTGGGTTTATACAACAAAAGCT +AGCTCTTGGAGGTTCCGTGGCTATAAAGATAACAGAACATTCTTGGAATGCTGATCTTTATAAGCTCATG +GGACACTTCGCATGGTGGACAGCCTTTGTTACTAATGTGAATGCGTCATCATCTGAAGCATTTTTAATTG +GATGTAATTATCTTGGCAAACCACGCGAACAAATAGATGGTTATGTCATGCATGCAAATTACATATTTTG +GAGGAATACAAATCCAATTCAGTTGTCTTCCTATTCTTTATTTGACATGAGTAAATTTCCCCTTAAATTA +AGGGGTACTGCTGTTATGTCTTTAAAAGAAGGTCAAATCAATGATATGATTTTATCTCTTCTTAGTAAAG +GTAGACTTATAATTAGAGAAAACAACAGAGTTGTTATTTCTAGTGATGTTCTTGTTAACAACTAAACGAA +CAATGTTTGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACCAGAACTCA +ATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGACAAAGTTTTCAGATCCTCA +GTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCCAATGTTACTTGGTTCCATGCTATACATG +TCTCTGGGACCAATGGTACTAAGAGGTTTGATAACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGC +TTCCACTGAGAAGTCTAACATAATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCC +CTACTTATTGTTAATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATGATCCAT +TTTTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTATTCTAGTGC +GAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAAGGAAAACAGGGTAATTTC +AAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTATTTTAAAATATATTCTAAGCACACGCCTA +TTAATTTAGTGCGTGATCTCCCTCAGGGTTTTTCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTAT +TAACATCACTAGGTTTCAAACTTTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCA +GGTTGGACAGCTGGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATA +ATGAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAGTGTACGTT +GAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTCCAACCAACAGAATCTATT +GTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAAGTTTTTAACGCCACCAGATTTGCATCTG +TTTATGCTTGGAACAGGAAGAGAATCAGCAACTGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATC +ATTTTCCACTTTTAAGTGTTATGGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTAT +GCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTG +ATTATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAATCTTGATTC +TAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAATCTCAAACCTTTTGAGAGA +GATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGTAATGGTGTTGAAGGTTTTAATTGTTACT +TTCCTTTACAATCATATGGTTTCCAACCCACTAATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACT +TTCTTTTGAACTTCTACATGCACCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAAC +AAATGTGTCAATTTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTC +TGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAGACACTTGA +GATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCAGGAACAAATACTTCTAAC +CAGGTTGCTGTTCTTTATCAGGATGTTAACTGCACAGAAGTCCCTGTTGCTATTCATGCAGATCAACTTA +CTCCTACTTGGCGTGTTTATTCTACAGGTTCTAATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGC +TGAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACT +CAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTG +GTGCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATTAGTGTTAC +CACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATGTACATTTGTGGTGATTCA +ACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGTACACAATTAAACCGTGCTTTAACTGGAA +TAGCTGTTGAACAAGACAAAAACACCCAAGAAGTTTTTGCACAAGTCAAACAAATTTACAAAACACCACC +AATTAAAGATTTTGGTGGTTTTAATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCA +TTTATTGAAGATCTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATT +GCCTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTTTTGCCACC +TTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGTACAATCACTTCTGGTTGG +ACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATGCAAATGGCTTATAGGTTTAATGGTATTG +GAGTTACACAGAATGTTCTCTATGAGAACCAAAAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAA +AATTCAAGACTCACTTTCTTCCACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCA +CAAGCTTTAAACACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATA +TCCTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGACTTCAAAG +TTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCTTCTGCTAATCTTGCTGCT +ACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTTGATTTTTGTGGAAAGGGCTATCATCTTA +TGTCCTTCCCTCAGTCAGCACCTCATGGTGTAGTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAA +GAACTTCACAACTGCTCCTGCCATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTT +TCAAATGGCACACACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACA +CATTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCTTTGCAACC +TGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACATCACCAGATGTTGATTTA +GGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAAAAAGAAATTGACCGCCTCAATGAGGTTG +CCAAGAATTTAAATGAATCTCTCATCGATCTCCAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCC +ATGGTACATTTGGCTAGGTTTTATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGT +ATGACCAGTTGCTGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACG +ACTCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACATAAACGAACTTATGGATTTGTTTATGAGA +ATCTTCACAATTGGAACTGTAACTTTGAAGCAAGGTGAAATCAAGGATGCTACTCCTTCAGATTTTGTTC +GCGCTACTGCAACGATACCGATACAAGCCTCACTCCCTTTCGGATGGCTTATTGTTGGCGTTGCACTTCT +TGCTGTTTTTCAGAGCGCTTCCAAAATCATAACCCTCAAAAAGAGATGGCAACTAGCACTCTCCAAGGGT +GTTCACTTTGTTTGCAACTTGCTGTTGTTGTTTGTAACAGTTTACTCACACCTTTTGCTCGTTGCTGCTG +GCCTTGAAGCCCCTTTTCTCTATCTTTATGCTTTAGTCTACTTCTTGCAGAGTATAAACTTTGTAAGAAT +AATAATGAGGCTTTGGCTTTGCTGGAAATGCCGTTCCAAAAACCCATTACTTTATGATGCCAACTATTTT +CTTTGCTGGCATACTAATTGTTACGACTATTGTATACCTTACAATAGTGTAACTTCTTCAATTGTCATTA +CTTCAGGTGATGGCACAACAAGTCCTATTTCTGAACATGACTACCAGATTGGTGGTTATACTGAAAAATG +GGAATCTGGAGTAAAAGACTGTGTTGTATTACACAGTTACTTCACTTCAGACTATTACCAGCTGTACTCA +ACTCAATTGAGTACAGACACTGGTGTTGAACATGTTACCTTCTTCATCTACAATAAAATTGTTGATGAGC +CTGAAGAACATGTCCAAATTCACACAATCGACGGTTCATCCGGAGTTGTTAATCCAGTAATGGAACCAAT +TTATGATGAACCGACGACGACTACTAGCGTGCCTTTGTAAGCACAAGCTGATGAGTACGAACTTATGTAC +TCATTCGTTTCGGAAGAGACAGGTACGTTAATAGTTAATAGCGTACTTCTTTTTCTTGCTTTCGTGGTAT +TCTTGCTAGTTACACTAGCCATCCTTACTGCGCTTCGATTGTGTGCGTACTGCTGCAATATTGTTAACGT +GAGTCTTGTAAAACCTTCTTTTTACGTTTACTCTCGTGTTAAAAATCTGAATTCTTCTAGAGTTCCTGAT +CTTCTGGTCTAAACGAACTAAATATTATATTAGTTTTTCTGTTTGGAACTTTAATTTTAGCCATGGCAGA +TTCCAACGGTACTATTACCGTTGAAGAGCTTAAAAAGCTCCTTGAACAATGGAACCTAGTAATAGGTTTC +CTATTCCTTACATGGATTTGTCTTCTACAATTTGCCTATGCCAACAGGAATAGGTTTTTGTATATAATTA +AGTTAATTTTCCTCTGGCTGTTATGGCCAGTAACTTTAGCTTGTTTTGTGCTTGCTGCTGTTTACAGAAT +AAATTGGATCACCGGTGGAATTGCTATCGCAATGGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTC +ATTGCTTCTTTCAGACTGTTTGCGCGTACGCGTTCCATGTGGTCATTCAATCCAGAAACTAACATTCTTC +TCAACGTGCCACTCCATGGCACTATTCTGACCAGACCGCTTCTAGAAAGTGAACTCGTAATCGGAGCTGT +GATCCTTCGTGGACATCTTCGTATTGCTGGACACCATCTAGGACGCTGTGACATCAAGGACCTGCCTAAA +GAAATCACTGTTGCTACATCACGAACGCTTTCTTATTACAAATTGGGAGCTTCGCAGCGTGTAGCAGGTG +ACTCAGGTTTTGCTGCATACAGTCGCTACAGGATTGGCAACTATAAATTAAACACAGACCATTCCAGTAG +CAGTGACAATATTGCTTTGCTTGTACAGTAAGTGACAACAGATGTTTCATCTCGTTGACTTTCAGGTTAC +TATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATA +AACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAAC +CAATGGAGATTGATTAAACGAACATGAAAATTATTCTTTTCTTGGCACTGATAACACTCGCTACTTGTGA +GCTTTATCACTACCAAGAGTGTGTTAGAGGTACAACAGTACTTTTAAAAGAACCTTGCTCTTCTGGAACA +TACGAGGGCAATTCACCATTTCATCCTCTAGCTGATAACAAATTTGCACTGACTTGCTTTAGCACTCAAT +TTGCTTTTGCTTGTCCTGACGGCGTAAAACACGTCTATCAGTTACGTGCCAGATCAGTTTCACCTAAACT +GTTCATCAGACAAGAGGAAGTTCAAGAACTTTACTCTCCAATTTTTCTTATTGTTGCGGCAATAGTGTTT +ATAACACTTTGCTTCACACTCAAAAGAAAGACAGAATGATTGAACTTTCATTAATTGACTTCTATTTGTG +CTTTTTAGCCTTTCTGCTATTCCTTGTTTTAATTATGCTTATTATCTTTTGGTTCTCACTTGAACTGCAA +GATCATAATGAAACTTGTCACGCCTAAACGAACATGAAATTTCTTGTTTTCTTAGGAATCATCACAACTG +TAGCTGCATTTCACCAAGAATGTAGTTTACAGTCATGTACTCAACATCAACCATATGTAGTTGATGACCC +GTGTCCTATTCACTTCTATTCTAAATGGTATATTAGAGTAGGAGCTAGAAAATCAGCACCTTTAATTGAA +TTGTGCGTGGATGAGGCTGGTTCTAAATCACCCATTCAGTACATCGATATCGGTAATTATACAGTTTCCT +GTTTACCTTTTACAATTAATTGCCAGGAACCTAAATTGGGTAGTCTTGTAGTGCGTTGTTCGTTCTATGA +AGACTTTTTAGAGTATCATGACGTTCGTGTTGTTTTAGATTTCATCTAAACGAACAAACTAAAATGTCTG +ATAATGGACCCCAAAATCAGCGAAATGCACCCCGCATTACGTTTGGTGGACCCTCAGATTCAACTGGCAG +TAACCAGAATGGAGAACGCAGTGGGGCGCGATCAAAACAACGTCGGCCCCAAGGTTTACCCAATAATACT +GCGTCTTGGTTCACCGCTCTCACTCAACATGGCAAGGAAGACCTTAAATTCCCTCGAGGACAAGGCGTTC +CAATTAACACCAATAGCAGTCCAGATGACCAAATTGGCTACTACCGAAGAGCTACCAGACGAATTCGTGG +TGGTGACGGTAAAATGAAAGATCTCAGTCCAAGATGGTATTTCTACTACCTAGGAACTGGGCCAGAAGCT +GGACTTCCCTATGGTGCTAACAAAGACGGCATCATATGGGTTGCAACTGAGGGAGCCTTGAATACACCAA +AAGATCACATTGGCACCCGCAATCCTGCTAACAATGCTGCAATCGTGCTACAACTTCCTCAAGGAACAAC +ATTGCCAAAAGGCTTCTACGCAGAAGGGAGCAGAGGCGGCAGTCAAGCCTCTTCTCGTTCCTCATCACGT +AGTCGCAACAGTTCAAGAAATTCAACTCCAGGCAGCAGTAGGGGAACTTCTCCTGCTAGAATGGCTGGCA +ATGGCGGTGATGCTGCTCTTGCTTTGCTGCTGCTTGACAGATTGAACCAGCTTGAGAGCAAAATGTCTGG +TAAAGGCCAACAACAACAAGGCCAAACTGTCACTAAGAAATCTGCTGCTGAGGCTTCTAAGAAGCCTCGG +CAAAAACGTACTGCCACTAAAGCATACAATGTAACACAAGCTTTCGGCAGACGTGGTCCAGAACAAACCC +AAGGAAATTTTGGGGACCAGGAACTAATCAGACAAGGAACTGATTACAAACATTGGCCGCAAATTGCACA +ATTTGCCCCCAGCGCTTCAGCGTTCTTCGGAATGTCGCGCATTGGCATGGAAGTCACACCTTCGGGAACG +TGGTTGACCTACACAGGTGCCATCAAATTGGATGACAAAGATCCAAATTTCAAAGATCAAGTCATTTTGC +TGAATAAGCATATTGACGCATACAAAACATTCCCACCAACAGAGCCTAAAAAGGACAAAAAGAAGAAGGC +TGATGAAACTCAAGCCTTACCGCAGAGACAGAAGAAACAGCAAACTGTGACTCTTCTTCCTGCTGCAGAT +TTGGATGATTTCTCCAAACAATTGCAACAATCCATGAGCAGTGCTGACTCAACTCAGGCCTAAACTCATG +CAGACCACACAAGGCAGATGGGCTATATAAACGTTTTCGCTTTTCCGTTTACGATATATAGTCTACTCTT +GTGCAGAATGAATTCTCGTAACTACATAGCACAAGTAGATGTAGTTAACTTTAATCTCACATAGCAATCT +TTAATCAGTGTGTAACATTAGGGAGGACTTGAAAGAGCCACCACATTTTCACCGAGGCCACGCGGAGTAC +GATCGAGTGTACAGTGAACAATGCTAGGGAGAGCTGCCTATATGGAAGAGCCCTAATGTGTAAAATTAAT +TTTAGTAGTGCTATCCCCATGTGATTTTAATAGCTTCTTAGGAGAATGACAAAAAAAAAAAAAAAAAAAA +AAAAAAAAAAAAA diff --git a/test/data/primer-schemes/schemes/sars-cov-2/eden/2500/v1.0.0/scheme.bed b/test/data/primer-schemes/schemes/sars-cov-2/eden/2500/v1.0.0/scheme.bed new file mode 100644 index 0000000..e75e9b3 --- /dev/null +++ b/test/data/primer-schemes/schemes/sars-cov-2/eden/2500/v1.0.0/scheme.bed @@ -0,0 +1,28 @@ +MN908947.3 31 55 SARS2_1_LEFT_1 1 + +MN908947.3 2569 2593 SARS2_1_RIGHT_1 1 - +MN908947.3 1876 1898 SARS2_2_LEFT_1 2 + +MN908947.3 4429 4451 SARS2_2_RIGHT_1 2 - +MN908947.3 4295 4322 SARS2_3_LEFT_1 1 + +MN908947.3 6847 6874 SARS2_3_RIGHT_1 1 - +MN908947.3 6287 6311 SARS2_4_LEFT_1 2 + +MN908947.3 8828 8852 SARS2_4_RIGHT_1 2 - +MN908947.3 8596 8620 SARS2_5_LEFT_1 1 + +MN908947.3 11049 11075 SARS2_5_RIGHT_1 1 - +MN908947.3 10363 10385 SARS2_6_LEFT_1 2 + +MN908947.3 12780 12803 SARS2_6_RIGHT_1 2 - +MN908947.3 12711 12733 SARS2_7_LEFT_1 1 + +MN908947.3 15225 15247 SARS2_7_RIGHT_1 1 - +MN908947.3 14546 14571 SARS2_8_LEFT_1 2 + +MN908947.3 17131 17153 SARS2_8_RIGHT_1 2 - +MN908947.3 16847 16872 SARS2_9_LEFT_1 1 + +MN908947.3 19254 19279 SARS2_9_RIGHT_1 1 - +MN908947.3 18897 18919 SARS2_10_LEFT_1 2 + +MN908947.3 21428 21456 SARS2_10_RIGHT_1 2 - +MN908947.3 21358 21387 SARS2_11_LEFT_1 1 + +MN908947.3 23823 23848 SARS2_11_RIGHT_1 1 - +MN908947.3 23123 23145 SARS2_12_LEFT_1 2 + +MN908947.3 25647 25674 SARS2_12_RIGHT_1 2 - +MN908947.3 25602 25624 SARS2_13_LEFT_1 1 + +MN908947.3 28146 28173 SARS2_13_RIGHT_1 1 - +MN908947.3 27447 27472 SARS2_14_LEFT_1 2 + +MN908947.3 29837 29867 SARS2_14_RIGHT_1 2 - diff --git a/test/data/primer-schemes/midnight/v1/info.yml b/test/data/primer-schemes/schemes/sars-cov-2/midnight/1200/v1.0.0/info.yml similarity index 50% rename from test/data/primer-schemes/midnight/v1/info.yml rename to test/data/primer-schemes/schemes/sars-cov-2/midnight/1200/v1.0.0/info.yml index 79c1704..b7d340f 100644 --- a/test/data/primer-schemes/midnight/v1/info.yml +++ b/test/data/primer-schemes/schemes/sars-cov-2/midnight/1200/v1.0.0/info.yml @@ -1,20 +1,23 @@ -schema_version: 0.9.0 -name: midnight-v1 +schema_version: 1.0.0a organism: sars-cov-2 +name: midnight +amplicon_size: 1200 +version: v1.0.0 aliases: - midnight-ont-v1 +- Midnight-ONT/V1 - V1200 developers: -- person_name: Nikki Freed -- person_name: Olin Silander +- Nikki Freed +- Olin Silander vendors: - organisation_name: Oxford Nanopore Technologies kit_name: MRT001.10 - organisation_name: Integrated DNA Technologies -amplicon_size: 1200 -repository_url: https://github.com/pha4ge/primer-schemes/tree/main/sars-cov-2/midnight/v1 +definition_url: https://github.com/pha4ge/primer-schemes/tree/main/sars-cov-2/midnight/v1 citations: - https://dx.doi.org/10.17504/protocols.io.bwyppfvn -primer_scheme_status: DEPRECATED -primer_checksum: primaschema:e1303ce0367cc245 -reference_checksum: primaschema:7d5621cd3b3e498d +license: CC-BY-4.0 +status: DEPRECATED +primer_checksum: primaschema:5f4389079f1acc9c +reference_checksum: primaschema:b1acd7163146bf17 diff --git a/test/data/primer-schemes/schemes/sars-cov-2/midnight/1200/v1.0.0/primer.bed b/test/data/primer-schemes/schemes/sars-cov-2/midnight/1200/v1.0.0/primer.bed new file mode 100644 index 0000000..a7c7c4a --- /dev/null +++ b/test/data/primer-schemes/schemes/sars-cov-2/midnight/1200/v1.0.0/primer.bed @@ -0,0 +1,58 @@ +MN908947.3 30 54 SARS-CoV-2_1_LEFT_1 1 + ACCAACCAACTTTCGATCTCTTGT +MN908947.3 1183 1205 SARS-CoV-2_1_RIGHT_1 1 - GGTTGCATTCATTTGGTGACGC +MN908947.3 1100 1128 SARS-CoV-2_2_LEFT_1 2 + CCATAATCAAGACTATTCAACCAAGGGT +MN908947.3 2244 2266 SARS-CoV-2_2_RIGHT_1 2 - ACAGGTGACAATTTGTCCACCG +MN908947.3 2153 2179 SARS-CoV-2_3_LEFT_1 1 + GGCTTGAAGAGAAGTTTAAGGAAGGT +MN908947.3 3235 3257 SARS-CoV-2_3_RIGHT_1 1 - GATTGTCCTCACTGCCGTCTTG +MN908947.3 3144 3166 SARS-CoV-2_4_LEFT_1 2 + GGAATTTGGTGCCACTTCTGCT +MN908947.3 4240 4262 SARS-CoV-2_4_RIGHT_1 2 - CCTGACCCGGGTAAGTGGTTAT +MN908947.3 4167 4189 SARS-CoV-2_5_LEFT_1 1 + ACCTACTAAAAAGGCTGGTGGC +MN908947.3 5337 5359 SARS-CoV-2_5_RIGHT_1 1 - AGCATCTTGTAGAGCAGGTGGA +MN908947.3 5257 5286 SARS-CoV-2_6_LEFT_1 2 + ACTTCTATTAAATGGGCAGATAACAACTG +MN908947.3 6358 6380 SARS-CoV-2_6_RIGHT_1 2 - GATTATCCATTCCCTGCGCGTC +MN908947.3 6283 6307 SARS-CoV-2_7_LEFT_1 1 + ACCTGGTGTATACGTTGTCTTTGG +MN908947.3 7379 7401 SARS-CoV-2_7_RIGHT_1 1 - GCTGAAATCGGGGCCATTTGTA +MN908947.3 7298 7328 SARS-CoV-2_8_LEFT_1 2 + CAATCATGCAATTGTTTTTCAGCTATTTTG +MN908947.3 8363 8385 SARS-CoV-2_8_RIGHT_1 2 - TGACTTTTTGCTACCTGCGCAT +MN908947.3 8253 8282 SARS-CoV-2_9_LEFT_1 1 + AGAAGTTACTGGCGATAGTTGTAATAACT +MN908947.3 9378 9400 SARS-CoV-2_9_RIGHT_1 1 - TGCTGATATGTCCAAAGCACCA +MN908947.3 9303 9327 SARS-CoV-2_10_LEFT_1 2 + TTTACCAGGAGTTTTCTGTGGTGT +MN908947.3 10429 10451 SARS-CoV-2_10_RIGHT_1 2 - TGGGCCTCATAGCACATTGGTA +MN908947.3 10343 10370 SARS-CoV-2_11_LEFT_1 1 + AGACACCTAAGTATAAGTTTGTTCGCA +MN908947.3 11447 11469 SARS-CoV-2_11_RIGHT_1 1 - GCCCACATGGAAATGGCTTGAT +MN908947.3 11372 11394 SARS-CoV-2_12_LEFT_1 2 + ATGGTGCTAGGAGAGTGTGGAC +MN908947.3 12538 12560 SARS-CoV-2_12_RIGHT_1 2 - GGATTTCCCACAATGCTGATGC +MN908947.3 12450 12473 SARS-CoV-2_13_LEFT_1 1 + ACCTCTTACAACAGCAGCCAAAC +MN908947.3 13599 13621 SARS-CoV-2_13_RIGHT_1 1 - CGTCCTTTTCTTGGAAGCGACA +MN908947.3 13509 13532 SARS-CoV-2_14_LEFT_1 2 + ACAGGCACTAGTACTGATGTCGT +MN908947.3 14619 14641 SARS-CoV-2_14_RIGHT_1 2 - GTGCAGCTACTGAAAAGCACGT +MN908947.3 14540 14568 SARS-CoV-2_15_LEFT_1 1 + TTTTAAGGAATTACTTGTGTATGCTGCT +MN908947.3 15713 15735 SARS-CoV-2_15_RIGHT_1 1 - ACACACAACAGCATCGTCAGAG +MN908947.3 15608 15634 SARS-CoV-2_16_LEFT_1 2 + ACAACACAGACTTTATGAGTGTCTCT +MN908947.3 16698 16720 SARS-CoV-2_16_RIGHT_1 2 - CTCTGTCAGACAGCACTTCACG +MN908947.3 16624 16647 SARS-CoV-2_17_LEFT_1 1 + TCAAGCTTTTTGCAGCAGAAACG +MN908947.3 17732 17754 SARS-CoV-2_17_RIGHT_1 1 - CCAAGCAGGGTTACGTGTAAGG +MN908947.3 17622 17649 SARS-CoV-2_18_LEFT_1 2 + GCACATAAAGACAAATCAGCTCAATGC +MN908947.3 18684 18706 SARS-CoV-2_18_RIGHT_1 2 - TGTCTGAAGCAGTGGAAAAGCA +MN908947.3 18596 18618 SARS-CoV-2_19_LEFT_1 1 + GGCACATGGCTTTGAGTTGACA +MN908947.3 19655 19678 SARS-CoV-2_19_RIGHT_1 1 - CCTGTTGTCCATCAAAGTGTCCC +MN908947.3 19574 19604 SARS-CoV-2_20_LEFT_1 2 + ACAATTTGATACTTATAACCTCTGGAACAC +MN908947.3 20676 20698 SARS-CoV-2_20_RIGHT_1 2 - GATTAGGCATAGCAACACCCGG +MN908947.3 20553 20581 SARS-CoV-2_21_LEFT_1 1 + TCTGTAGTTTCTAAGGTTGTCAAAGTGA +MN908947.3 21620 21642 SARS-CoV-2_21_RIGHT_1 1 - GCAGGGGGTAATTGAGTTCTGG +MN908947.3 21532 21562 SARS-CoV-2_22_LEFT_1 2 + GTGATGTTCTTGTTAACAACTAAACGAACA +MN908947.3 22590 22612 SARS-CoV-2_22_RIGHT_1 2 - AACAGATGCAAATCTGGTGGCG +MN908947.3 22511 22537 SARS-CoV-2_23_LEFT_1 1 + ACTTTAGAGTCCAACCAACAGAATCT +MN908947.3 23609 23631 SARS-CoV-2_23_RIGHT_1 1 - TGACTAGCTACACTACGTGCCC +MN908947.3 23518 23544 SARS-CoV-2_24_LEFT_1 2 + GCTGAACATGTCAACAACTCATATGA +MN908947.3 24714 24736 SARS-CoV-2_24_RIGHT_1 2 - ATGAGGTGCTGACTGAGGGAAG +MN908947.3 24633 24658 SARS-CoV-2_25_LEFT_1 1 + TGCTGCTACTAAAATGTCAGAGTGT +MN908947.3 25768 25790 SARS-CoV-2_25_RIGHT_1 1 - CATTTCCAGCAAAGCCAAAGCC +MN908947.3 25690 25712 SARS-CoV-2_26_LEFT_1 2 + GCCTTGAAGCCCCTTTTCTCTA +MN908947.3 26835 26857 SARS-CoV-2_26_RIGHT_1 2 - AATGACCACATGGAACGCGTAC +MN908947.3 26744 26766 SARS-CoV-2_27_LEFT_1 1 + TGGATCACCGGTGGAATTGCTA +MN908947.3 27872 27894 SARS-CoV-2_27_RIGHT_1 1 - TGTTCGTTTAGGCGTGACAAGT +MN908947.3 27784 27808 SARS-CoV-2_28_LEFT_1 2 + TTTGTGCTTTTTAGCCTTTCTGCT +MN908947.3 28985 29007 SARS-CoV-2_28_RIGHT_1 2 - GTTTGGCCTTGTTGTTGTTGGC +MN908947.3 28677 28699 SARS-CoV-2_29_LEFT_1 1 + TGAGGGAGCCTTGAATACACCA +MN908947.3 29768 29790 SARS-CoV-2_29_RIGHT_1 1 - TAGGCAGCTCTCCCTAGCATTG diff --git a/test/data/primer-schemes/schemes/sars-cov-2/midnight/1200/v1.0.0/primer.svg b/test/data/primer-schemes/schemes/sars-cov-2/midnight/1200/v1.0.0/primer.svg new file mode 100644 index 0000000..b7d853c --- /dev/null +++ b/test/data/primer-schemes/schemes/sars-cov-2/midnight/1200/v1.0.0/primer.svg @@ -0,0 +1 @@ +12pool02,0004,0006,0008,00010,00012,00014,00016,00018,00020,00022,00024,00026,00028,00030,000MN908947.3+-strand \ No newline at end of file diff --git a/test/data/primer-schemes/midnight/v1/reference.fasta b/test/data/primer-schemes/schemes/sars-cov-2/midnight/1200/v1.0.0/reference.fasta similarity index 100% rename from test/data/primer-schemes/midnight/v1/reference.fasta rename to test/data/primer-schemes/schemes/sars-cov-2/midnight/1200/v1.0.0/reference.fasta diff --git a/test/data/primer-schemes/schemes/sars-cov-2/midnight/1200/v1.0.0/scheme.bed b/test/data/primer-schemes/schemes/sars-cov-2/midnight/1200/v1.0.0/scheme.bed new file mode 100644 index 0000000..888f3e9 --- /dev/null +++ b/test/data/primer-schemes/schemes/sars-cov-2/midnight/1200/v1.0.0/scheme.bed @@ -0,0 +1,58 @@ +MN908947.3 30 54 SARS-CoV-2_1_LEFT_1 1 + +MN908947.3 1183 1205 SARS-CoV-2_1_RIGHT_1 1 - +MN908947.3 1100 1128 SARS-CoV-2_2_LEFT_1 2 + +MN908947.3 2244 2266 SARS-CoV-2_2_RIGHT_1 2 - +MN908947.3 2153 2179 SARS-CoV-2_3_LEFT_1 1 + +MN908947.3 3235 3257 SARS-CoV-2_3_RIGHT_1 1 - +MN908947.3 3144 3166 SARS-CoV-2_4_LEFT_1 2 + +MN908947.3 4240 4262 SARS-CoV-2_4_RIGHT_1 2 - +MN908947.3 4167 4189 SARS-CoV-2_5_LEFT_1 1 + +MN908947.3 5337 5359 SARS-CoV-2_5_RIGHT_1 1 - +MN908947.3 5257 5286 SARS-CoV-2_6_LEFT_1 2 + +MN908947.3 6358 6380 SARS-CoV-2_6_RIGHT_1 2 - +MN908947.3 6283 6307 SARS-CoV-2_7_LEFT_1 1 + +MN908947.3 7379 7401 SARS-CoV-2_7_RIGHT_1 1 - +MN908947.3 7298 7328 SARS-CoV-2_8_LEFT_1 2 + +MN908947.3 8363 8385 SARS-CoV-2_8_RIGHT_1 2 - +MN908947.3 8253 8282 SARS-CoV-2_9_LEFT_1 1 + +MN908947.3 9378 9400 SARS-CoV-2_9_RIGHT_1 1 - +MN908947.3 9303 9327 SARS-CoV-2_10_LEFT_1 2 + +MN908947.3 10429 10451 SARS-CoV-2_10_RIGHT_1 2 - +MN908947.3 10343 10370 SARS-CoV-2_11_LEFT_1 1 + +MN908947.3 11447 11469 SARS-CoV-2_11_RIGHT_1 1 - +MN908947.3 11372 11394 SARS-CoV-2_12_LEFT_1 2 + +MN908947.3 12538 12560 SARS-CoV-2_12_RIGHT_1 2 - +MN908947.3 12450 12473 SARS-CoV-2_13_LEFT_1 1 + +MN908947.3 13599 13621 SARS-CoV-2_13_RIGHT_1 1 - +MN908947.3 13509 13532 SARS-CoV-2_14_LEFT_1 2 + +MN908947.3 14619 14641 SARS-CoV-2_14_RIGHT_1 2 - +MN908947.3 14540 14568 SARS-CoV-2_15_LEFT_1 1 + +MN908947.3 15713 15735 SARS-CoV-2_15_RIGHT_1 1 - +MN908947.3 15608 15634 SARS-CoV-2_16_LEFT_1 2 + +MN908947.3 16698 16720 SARS-CoV-2_16_RIGHT_1 2 - +MN908947.3 16624 16647 SARS-CoV-2_17_LEFT_1 1 + +MN908947.3 17732 17754 SARS-CoV-2_17_RIGHT_1 1 - +MN908947.3 17622 17649 SARS-CoV-2_18_LEFT_1 2 + +MN908947.3 18684 18706 SARS-CoV-2_18_RIGHT_1 2 - +MN908947.3 18596 18618 SARS-CoV-2_19_LEFT_1 1 + +MN908947.3 19655 19678 SARS-CoV-2_19_RIGHT_1 1 - +MN908947.3 19574 19604 SARS-CoV-2_20_LEFT_1 2 + +MN908947.3 20676 20698 SARS-CoV-2_20_RIGHT_1 2 - +MN908947.3 20553 20581 SARS-CoV-2_21_LEFT_1 1 + +MN908947.3 21620 21642 SARS-CoV-2_21_RIGHT_1 1 - +MN908947.3 21532 21562 SARS-CoV-2_22_LEFT_1 2 + +MN908947.3 22590 22612 SARS-CoV-2_22_RIGHT_1 2 - +MN908947.3 22511 22537 SARS-CoV-2_23_LEFT_1 1 + +MN908947.3 23609 23631 SARS-CoV-2_23_RIGHT_1 1 - +MN908947.3 23518 23544 SARS-CoV-2_24_LEFT_1 2 + +MN908947.3 24714 24736 SARS-CoV-2_24_RIGHT_1 2 - +MN908947.3 24633 24658 SARS-CoV-2_25_LEFT_1 1 + +MN908947.3 25768 25790 SARS-CoV-2_25_RIGHT_1 1 - +MN908947.3 25690 25712 SARS-CoV-2_26_LEFT_1 2 + +MN908947.3 26835 26857 SARS-CoV-2_26_RIGHT_1 2 - +MN908947.3 26744 26766 SARS-CoV-2_27_LEFT_1 1 + +MN908947.3 27872 27894 SARS-CoV-2_27_RIGHT_1 1 - +MN908947.3 27784 27808 SARS-CoV-2_28_LEFT_1 2 + +MN908947.3 28985 29007 SARS-CoV-2_28_RIGHT_1 2 - +MN908947.3 28677 28699 SARS-CoV-2_29_LEFT_1 1 + +MN908947.3 29768 29790 SARS-CoV-2_29_RIGHT_1 1 - diff --git a/test/data/primer-schemes/midnight/v2/info.yml b/test/data/primer-schemes/schemes/sars-cov-2/midnight/1200/v2.0.0/info.yml similarity index 62% rename from test/data/primer-schemes/midnight/v2/info.yml rename to test/data/primer-schemes/schemes/sars-cov-2/midnight/1200/v2.0.0/info.yml index 47c95f2..8354d30 100644 --- a/test/data/primer-schemes/midnight/v2/info.yml +++ b/test/data/primer-schemes/schemes/sars-cov-2/midnight/1200/v2.0.0/info.yml @@ -1,24 +1,27 @@ -schema_version: 0.9.0 -name: midnight-v2 +schema_version: 1.0.0a organism: sars-cov-2 +name: midnight +amplicon_size: 1200 +version: v2.0.0 aliases: - midnight-ont-v2 - midnight-idt-v1 +- Midnight-ONT/V2 derived_from: midnight-v1 developers: -- person_name: Nikki Freed -- person_name: Olin Silander +- Nikki Freed +- Olin Silander vendors: - organisation_name: Oxford Nanopore Technologies kit_name: MRT001.20 -amplicon_size: 1200 -repository_url: https://github.com/pha4ge/primer-schemes/tree/main/sars-cov-2/midnight/v2 +definition_url: https://github.com/pha4ge/primer-schemes/tree/main/sars-cov-2/midnight/v2 citations: - https://dx.doi.org/10.17504/protocols.io.bwyppfvn notes: - Accomodates Omicron BA.1 with single primer addition - https://twitter.com/freed_nikki/status/1464477522448433156 - Not considered a new version by Freed et al. and IDT despite additional primer -primer_scheme_status: DEPRECATED -primer_checksum: primaschema:8f733a1f180c435a -reference_checksum: primaschema:7d5621cd3b3e498d +license: CC-BY-4.0 +status: DEPRECATED +primer_checksum: primaschema:eafcbe457b8a2345 +reference_checksum: primaschema:b1acd7163146bf17 diff --git a/test/data/primer-schemes/schemes/sars-cov-2/midnight/1200/v2.0.0/primer.bed b/test/data/primer-schemes/schemes/sars-cov-2/midnight/1200/v2.0.0/primer.bed new file mode 100644 index 0000000..59d6310 --- /dev/null +++ b/test/data/primer-schemes/schemes/sars-cov-2/midnight/1200/v2.0.0/primer.bed @@ -0,0 +1,59 @@ +MN908947.3 30 54 SARS-CoV-2_1_LEFT_1 1 + ACCAACCAACTTTCGATCTCTTGT +MN908947.3 1183 1205 SARS-CoV-2_1_RIGHT_1 1 - GGTTGCATTCATTTGGTGACGC +MN908947.3 1100 1128 SARS-CoV-2_2_LEFT_1 2 + CCATAATCAAGACTATTCAACCAAGGGT +MN908947.3 2244 2266 SARS-CoV-2_2_RIGHT_1 2 - ACAGGTGACAATTTGTCCACCG +MN908947.3 2153 2179 SARS-CoV-2_3_LEFT_1 1 + GGCTTGAAGAGAAGTTTAAGGAAGGT +MN908947.3 3235 3257 SARS-CoV-2_3_RIGHT_1 1 - GATTGTCCTCACTGCCGTCTTG +MN908947.3 3144 3166 SARS-CoV-2_4_LEFT_1 2 + GGAATTTGGTGCCACTTCTGCT +MN908947.3 4240 4262 SARS-CoV-2_4_RIGHT_1 2 - CCTGACCCGGGTAAGTGGTTAT +MN908947.3 4167 4189 SARS-CoV-2_5_LEFT_1 1 + ACCTACTAAAAAGGCTGGTGGC +MN908947.3 5337 5359 SARS-CoV-2_5_RIGHT_1 1 - AGCATCTTGTAGAGCAGGTGGA +MN908947.3 5257 5286 SARS-CoV-2_6_LEFT_1 2 + ACTTCTATTAAATGGGCAGATAACAACTG +MN908947.3 6358 6380 SARS-CoV-2_6_RIGHT_1 2 - GATTATCCATTCCCTGCGCGTC +MN908947.3 6283 6307 SARS-CoV-2_7_LEFT_1 1 + ACCTGGTGTATACGTTGTCTTTGG +MN908947.3 7379 7401 SARS-CoV-2_7_RIGHT_1 1 - GCTGAAATCGGGGCCATTTGTA +MN908947.3 7298 7328 SARS-CoV-2_8_LEFT_1 2 + CAATCATGCAATTGTTTTTCAGCTATTTTG +MN908947.3 8363 8385 SARS-CoV-2_8_RIGHT_1 2 - TGACTTTTTGCTACCTGCGCAT +MN908947.3 8253 8282 SARS-CoV-2_9_LEFT_1 1 + AGAAGTTACTGGCGATAGTTGTAATAACT +MN908947.3 9378 9400 SARS-CoV-2_9_RIGHT_1 1 - TGCTGATATGTCCAAAGCACCA +MN908947.3 9303 9327 SARS-CoV-2_10_LEFT_1 2 + TTTACCAGGAGTTTTCTGTGGTGT +MN908947.3 10429 10451 SARS-CoV-2_10_RIGHT_1 2 - TGGGCCTCATAGCACATTGGTA +MN908947.3 10343 10370 SARS-CoV-2_11_LEFT_1 1 + AGACACCTAAGTATAAGTTTGTTCGCA +MN908947.3 11447 11469 SARS-CoV-2_11_RIGHT_1 1 - GCCCACATGGAAATGGCTTGAT +MN908947.3 11372 11394 SARS-CoV-2_12_LEFT_1 2 + ATGGTGCTAGGAGAGTGTGGAC +MN908947.3 12538 12560 SARS-CoV-2_12_RIGHT_1 2 - GGATTTCCCACAATGCTGATGC +MN908947.3 12450 12473 SARS-CoV-2_13_LEFT_1 1 + ACCTCTTACAACAGCAGCCAAAC +MN908947.3 13599 13621 SARS-CoV-2_13_RIGHT_1 1 - CGTCCTTTTCTTGGAAGCGACA +MN908947.3 13509 13532 SARS-CoV-2_14_LEFT_1 2 + ACAGGCACTAGTACTGATGTCGT +MN908947.3 14619 14641 SARS-CoV-2_14_RIGHT_1 2 - GTGCAGCTACTGAAAAGCACGT +MN908947.3 14540 14568 SARS-CoV-2_15_LEFT_1 1 + TTTTAAGGAATTACTTGTGTATGCTGCT +MN908947.3 15713 15735 SARS-CoV-2_15_RIGHT_1 1 - ACACACAACAGCATCGTCAGAG +MN908947.3 15608 15634 SARS-CoV-2_16_LEFT_1 2 + ACAACACAGACTTTATGAGTGTCTCT +MN908947.3 16698 16720 SARS-CoV-2_16_RIGHT_1 2 - CTCTGTCAGACAGCACTTCACG +MN908947.3 16624 16647 SARS-CoV-2_17_LEFT_1 1 + TCAAGCTTTTTGCAGCAGAAACG +MN908947.3 17732 17754 SARS-CoV-2_17_RIGHT_1 1 - CCAAGCAGGGTTACGTGTAAGG +MN908947.3 17622 17649 SARS-CoV-2_18_LEFT_1 2 + GCACATAAAGACAAATCAGCTCAATGC +MN908947.3 18684 18706 SARS-CoV-2_18_RIGHT_1 2 - TGTCTGAAGCAGTGGAAAAGCA +MN908947.3 18596 18618 SARS-CoV-2_19_LEFT_1 1 + GGCACATGGCTTTGAGTTGACA +MN908947.3 19655 19678 SARS-CoV-2_19_RIGHT_1 1 - CCTGTTGTCCATCAAAGTGTCCC +MN908947.3 19574 19604 SARS-CoV-2_20_LEFT_1 2 + ACAATTTGATACTTATAACCTCTGGAACAC +MN908947.3 20676 20698 SARS-CoV-2_20_RIGHT_1 2 - GATTAGGCATAGCAACACCCGG +MN908947.3 20553 20581 SARS-CoV-2_21_LEFT_1 1 + TCTGTAGTTTCTAAGGTTGTCAAAGTGA +MN908947.3 21620 21642 SARS-CoV-2_21_RIGHT_1 1 - GCAGGGGGTAATTGAGTTCTGG +MN908947.3 21532 21562 SARS-CoV-2_22_LEFT_1 2 + GTGATGTTCTTGTTAACAACTAAACGAACA +MN908947.3 22590 22612 SARS-CoV-2_22_RIGHT_1 2 - AACAGATGCAAATCTGGTGGCG +MN908947.3 22511 22537 SARS-CoV-2_23_LEFT_1 1 + ACTTTAGAGTCCAACCAACAGAATCT +MN908947.3 23609 23631 SARS-CoV-2_23_RIGHT_1 1 - TGACTAGCTACACTACGTGCCC +MN908947.3 23518 23544 SARS-CoV-2_24_LEFT_1 2 + GCTGAACATGTCAACAACTCATATGA +MN908947.3 24714 24736 SARS-CoV-2_24_RIGHT_1 2 - ATGAGGTGCTGACTGAGGGAAG +MN908947.3 24633 24658 SARS-CoV-2_25_LEFT_1 1 + TGCTGCTACTAAAATGTCAGAGTGT +MN908947.3 25768 25790 SARS-CoV-2_25_RIGHT_1 1 - CATTTCCAGCAAAGCCAAAGCC +MN908947.3 25690 25712 SARS-CoV-2_26_LEFT_1 2 + GCCTTGAAGCCCCTTTTCTCTA +MN908947.3 26835 26857 SARS-CoV-2_26_RIGHT_1 2 - AATGACCACATGGAACGCGTAC +MN908947.3 26744 26766 SARS-CoV-2_27_LEFT_1 1 + TGGATCACCGGTGGAATTGCTA +MN908947.3 27872 27894 SARS-CoV-2_27_RIGHT_1 1 - TGTTCGTTTAGGCGTGACAAGT +MN908947.3 27784 27808 SARS-CoV-2_28_LEFT_1 2 + TTTGTGCTTTTTAGCCTTTCTGCT +MN908947.3 27784 27808 SARS-CoV-2_28_LEFT_2 2 + TTTGTGCTTTTTAGCCTTTCTGTT +MN908947.3 28985 29007 SARS-CoV-2_28_RIGHT_1 2 - GTTTGGCCTTGTTGTTGTTGGC +MN908947.3 28677 28699 SARS-CoV-2_29_LEFT_1 1 + TGAGGGAGCCTTGAATACACCA +MN908947.3 29768 29790 SARS-CoV-2_29_RIGHT_1 1 - TAGGCAGCTCTCCCTAGCATTG diff --git a/test/data/primer-schemes/schemes/sars-cov-2/midnight/1200/v2.0.0/primer.svg b/test/data/primer-schemes/schemes/sars-cov-2/midnight/1200/v2.0.0/primer.svg new file mode 100644 index 0000000..e3c55af --- /dev/null +++ b/test/data/primer-schemes/schemes/sars-cov-2/midnight/1200/v2.0.0/primer.svg @@ -0,0 +1 @@ +12pool02,0004,0006,0008,00010,00012,00014,00016,00018,00020,00022,00024,00026,00028,00030,000MN908947.3+-strand \ No newline at end of file diff --git a/test/data/primer-schemes/midnight/v2/reference.fasta b/test/data/primer-schemes/schemes/sars-cov-2/midnight/1200/v2.0.0/reference.fasta similarity index 100% rename from test/data/primer-schemes/midnight/v2/reference.fasta rename to test/data/primer-schemes/schemes/sars-cov-2/midnight/1200/v2.0.0/reference.fasta diff --git a/test/data/primer-schemes/schemes/sars-cov-2/midnight/1200/v2.0.0/scheme.bed b/test/data/primer-schemes/schemes/sars-cov-2/midnight/1200/v2.0.0/scheme.bed new file mode 100644 index 0000000..236992d --- /dev/null +++ b/test/data/primer-schemes/schemes/sars-cov-2/midnight/1200/v2.0.0/scheme.bed @@ -0,0 +1,59 @@ +MN908947.3 30 54 SARS-CoV-2_1_LEFT_1 1 + +MN908947.3 1183 1205 SARS-CoV-2_1_RIGHT_1 1 - +MN908947.3 1100 1128 SARS-CoV-2_2_LEFT_1 2 + +MN908947.3 2244 2266 SARS-CoV-2_2_RIGHT_1 2 - +MN908947.3 2153 2179 SARS-CoV-2_3_LEFT_1 1 + +MN908947.3 3235 3257 SARS-CoV-2_3_RIGHT_1 1 - +MN908947.3 3144 3166 SARS-CoV-2_4_LEFT_1 2 + +MN908947.3 4240 4262 SARS-CoV-2_4_RIGHT_1 2 - +MN908947.3 4167 4189 SARS-CoV-2_5_LEFT_1 1 + +MN908947.3 5337 5359 SARS-CoV-2_5_RIGHT_1 1 - +MN908947.3 5257 5286 SARS-CoV-2_6_LEFT_1 2 + +MN908947.3 6358 6380 SARS-CoV-2_6_RIGHT_1 2 - +MN908947.3 6283 6307 SARS-CoV-2_7_LEFT_1 1 + +MN908947.3 7379 7401 SARS-CoV-2_7_RIGHT_1 1 - +MN908947.3 7298 7328 SARS-CoV-2_8_LEFT_1 2 + +MN908947.3 8363 8385 SARS-CoV-2_8_RIGHT_1 2 - +MN908947.3 8253 8282 SARS-CoV-2_9_LEFT_1 1 + +MN908947.3 9378 9400 SARS-CoV-2_9_RIGHT_1 1 - +MN908947.3 9303 9327 SARS-CoV-2_10_LEFT_1 2 + +MN908947.3 10429 10451 SARS-CoV-2_10_RIGHT_1 2 - +MN908947.3 10343 10370 SARS-CoV-2_11_LEFT_1 1 + +MN908947.3 11447 11469 SARS-CoV-2_11_RIGHT_1 1 - +MN908947.3 11372 11394 SARS-CoV-2_12_LEFT_1 2 + +MN908947.3 12538 12560 SARS-CoV-2_12_RIGHT_1 2 - +MN908947.3 12450 12473 SARS-CoV-2_13_LEFT_1 1 + +MN908947.3 13599 13621 SARS-CoV-2_13_RIGHT_1 1 - +MN908947.3 13509 13532 SARS-CoV-2_14_LEFT_1 2 + +MN908947.3 14619 14641 SARS-CoV-2_14_RIGHT_1 2 - +MN908947.3 14540 14568 SARS-CoV-2_15_LEFT_1 1 + +MN908947.3 15713 15735 SARS-CoV-2_15_RIGHT_1 1 - +MN908947.3 15608 15634 SARS-CoV-2_16_LEFT_1 2 + +MN908947.3 16698 16720 SARS-CoV-2_16_RIGHT_1 2 - +MN908947.3 16624 16647 SARS-CoV-2_17_LEFT_1 1 + +MN908947.3 17732 17754 SARS-CoV-2_17_RIGHT_1 1 - +MN908947.3 17622 17649 SARS-CoV-2_18_LEFT_1 2 + +MN908947.3 18684 18706 SARS-CoV-2_18_RIGHT_1 2 - +MN908947.3 18596 18618 SARS-CoV-2_19_LEFT_1 1 + +MN908947.3 19655 19678 SARS-CoV-2_19_RIGHT_1 1 - +MN908947.3 19574 19604 SARS-CoV-2_20_LEFT_1 2 + +MN908947.3 20676 20698 SARS-CoV-2_20_RIGHT_1 2 - +MN908947.3 20553 20581 SARS-CoV-2_21_LEFT_1 1 + +MN908947.3 21620 21642 SARS-CoV-2_21_RIGHT_1 1 - +MN908947.3 21532 21562 SARS-CoV-2_22_LEFT_1 2 + +MN908947.3 22590 22612 SARS-CoV-2_22_RIGHT_1 2 - +MN908947.3 22511 22537 SARS-CoV-2_23_LEFT_1 1 + +MN908947.3 23609 23631 SARS-CoV-2_23_RIGHT_1 1 - +MN908947.3 23518 23544 SARS-CoV-2_24_LEFT_1 2 + +MN908947.3 24714 24736 SARS-CoV-2_24_RIGHT_1 2 - +MN908947.3 24633 24658 SARS-CoV-2_25_LEFT_1 1 + +MN908947.3 25768 25790 SARS-CoV-2_25_RIGHT_1 1 - +MN908947.3 25690 25712 SARS-CoV-2_26_LEFT_1 2 + +MN908947.3 26835 26857 SARS-CoV-2_26_RIGHT_1 2 - +MN908947.3 26744 26766 SARS-CoV-2_27_LEFT_1 1 + +MN908947.3 27872 27894 SARS-CoV-2_27_RIGHT_1 1 - +MN908947.3 27784 27808 SARS-CoV-2_28_LEFT_1 2 + +MN908947.3 27784 27808 SARS-CoV-2_28_LEFT_2 2 + +MN908947.3 28985 29007 SARS-CoV-2_28_RIGHT_1 2 - +MN908947.3 28677 28699 SARS-CoV-2_29_LEFT_1 1 + +MN908947.3 29768 29790 SARS-CoV-2_29_RIGHT_1 1 - diff --git a/test/data/unordered/info.yml b/test/data/unordered/info.yml new file mode 100644 index 0000000..d6a4040 --- /dev/null +++ b/test/data/unordered/info.yml @@ -0,0 +1,22 @@ +schema_version: 1.0.0-alpha +name: artic +amplicon_size: 400 +version: v4.1 +organism: sars-cov-2 +aliases: +- ARTIC/V4.1 +developers: +- ARTIC network +vendors: +- organisation_name: IDT + kit_name: '10011442' +- organisation_name: Eurofins + home_page: https://eurofinsgenomics.com +definition_url: https://github.com/pha4ge/primer-schemes/tree/main/sars-cov-2/artic/v4.1 +source_url: https://github.com/quick-lab/primerschemes/tree/main/primerschemes/artic-sars-cov-2/400/v4.1.0 +citations: +- https://doi.org/10.1101%2F2020.09.04.283077 +derived_from: artic-v4 +license: CC-BY-SA-4.0 +primer_checksum: primaschema:8eaf6a2fb31f602a +reference_checksum: primaschema:b1acd7163146bf17 diff --git a/test/data/unordered/primer.bed b/test/data/unordered/primer.bed new file mode 100644 index 0000000..128618d --- /dev/null +++ b/test/data/unordered/primer.bed @@ -0,0 +1,4 @@ +MN908947.3 25 50 SARS-CoV-2_1_LEFT_1 1 + AACAAACCAACCAACTTTCGATCTC +MN908947.3 324 344 SARS-CoV-2_2_LEFT_1 2 + TTTACAGGTTCGCGACGTGC +MN908947.3 408 431 SARS-CoV-2_1_RIGHT_1 1 - CTTCTACTAAGCCACAAGTGCCA +MN908947.3 705 727 SARS-CoV-2_2_RIGHT_1 2 - ATAAGGATCAGTGCCAAGCTCG \ No newline at end of file diff --git a/test/data/unordered/reference.fasta b/test/data/unordered/reference.fasta new file mode 100644 index 0000000..e1cfd92 --- /dev/null +++ b/test/data/unordered/reference.fasta @@ -0,0 +1,429 @@ +>MN908947.3 +ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAA +CGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAAC +TAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTG +TTGCAGCCGATCATCAGCACATCTAGGTTTCGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTC +CCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTAC +GTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGG +CTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAAACGTTCGGAT +GCTCGAACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACTCGAAGGCATTCAGTACGGTC +GTAGTGGTGAGACACTTGGTGTCCTTGTCCCTCATGTGGGCGAAATACCAGTGGCTTACCGCAAGGTTCT +TCTTCGTAAGAACGGTAATAAAGGAGCTGGTGGCCATAGTTACGGCGCCGATCTAAAGTCATTTGACTTA +GGCGACGAGCTTGGCACTGATCCTTATGAAGATTTTCAAGAAAACTGGAACACTAAACATAGCAGTGGTG +TTACCCGTGAACTCATGCGTGAGCTTAACGGAGGGGCATACACTCGCTATGTCGATAACAACTTCTGTGG +CCCTGATGGCTACCCTCTTGAGTGCATTAAAGACCTTCTAGCACGTGCTGGTAAAGCTTCATGCACTTTG +TCCGAACAACTGGACTTTATTGACACTAAGAGGGGTGTATACTGCTGCCGTGAACATGAGCATGAAATTG +CTTGGTACACGGAACGTTCTGAAAAGAGCTATGAATTGCAGACACCTTTTGAAATTAAATTGGCAAAGAA +ATTTGACACCTTCAATGGGGAATGTCCAAATTTTGTATTTCCCTTAAATTCCATAATCAAGACTATTCAA +CCAAGGGTTGAAAAGAAAAAGCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCCAGTTGCGTCAC +CAAATGAATGCAACCAAATGTGCCTTTCAACTCTCATGAAGTGTGATCATTGTGGTGAAACTTCATGGCA +GACGGGCGATTTTGTTAAAGCCACTTGCGAATTTTGTGGCACTGAGAATTTGACTAAAGAAGGTGCCACT +ACTTGTGGTTACTTACCCCAAAATGCTGTTGTTAAAATTTATTGTCCAGCATGTCACAATTCAGAAGTAG +GACCTGAGCATAGTCTTGCCGAATACCATAATGAATCTGGCTTGAAAACCATTCTTCGTAAGGGTGGTCG +CACTATTGCCTTTGGAGGCTGTGTGTTCTCTTATGTTGGTTGCCATAACAAGTGTGCCTATTGGGTTCCA +CGTGCTAGCGCTAACATAGGTTGTAACCATACAGGTGTTGTTGGAGAAGGTTCCGAAGGTCTTAATGACA +ACCTTCTTGAAATACTCCAAAAAGAGAAAGTCAACATCAATATTGTTGGTGACTTTAAACTTAATGAAGA +GATCGCCATTATTTTGGCATCTTTTTCTGCTTCCACAAGTGCTTTTGTGGAAACTGTGAAAGGTTTGGAT +TATAAAGCATTCAAACAAATTGTTGAATCCTGTGGTAATTTTAAAGTTACAAAAGGAAAAGCTAAAAAAG +GTGCCTGGAATATTGGTGAACAGAAATCAATACTGAGTCCTCTTTATGCATTTGCATCAGAGGCTGCTCG +TGTTGTACGATCAATTTTCTCCCGCACTCTTGAAACTGCTCAAAATTCTGTGCGTGTTTTACAGAAGGCC +GCTATAACAATACTAGATGGAATTTCACAGTATTCACTGAGACTCATTGATGCTATGATGTTCACATCTG +ATTTGGCTACTAACAATCTAGTTGTAATGGCCTACATTACAGGTGGTGTTGTTCAGTTGACTTCGCAGTG +GCTAACTAACATCTTTGGCACTGTTTATGAAAAACTCAAACCCGTCCTTGATTGGCTTGAAGAGAAGTTT +AAGGAAGGTGTAGAGTTTCTTAGAGACGGTTGGGAAATTGTTAAATTTATCTCAACCTGTGCTTGTGAAA +TTGTCGGTGGACAAATTGTCACCTGTGCAAAGGAAATTAAGGAGAGTGTTCAGACATTCTTTAAGCTTGT +AAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGCCTTGAATTTA +GGTGAAACATTTGTCACGCACTCAAAGGGATTGTACAGAAAGTGTGTTAAATCCAGAGAAGAAACTGGCC +TACTCATGCCTCTAAAAGCCCCAAAAGAAATTATCTTCTTAGAGGGAGAAACACTTCCCACAGAAGTGTT +AACAGAGGAAGTTGTCTTGAAAACTGGTGATTTACAACCATTAGAACAACCTACTAGTGAAGCTGTTGAA +GCTCCATTGGTTGGTACACCAGTTTGTATTAACGGGCTTATGTTGCTCGAAATCAAAGACACAGAAAAGT +ACTGTGCCCTTGCACCTAATATGATGGTAACAAACAATACCTTCACACTCAAAGGCGGTGCACCAACAAA +GGTTACTTTTGGTGATGACACTGTGATAGAAGTGCAAGGTTACAAGAGTGTGAATATCACTTTTGAACTT +GATGAAAGGATTGATAAAGTACTTAATGAGAAGTGCTCTGCCTATACAGTTGAACTCGGTACAGAAGTAA +ATGAGTTCGCCTGTGTTGTGGCAGATGCTGTCATAAAAACTTTGCAACCAGTATCTGAATTACTTACACC +ACTGGGCATTGATTTAGATGAGTGGAGTATGGCTACATACTACTTATTTGATGAGTCTGGTGAGTTTAAA +TTGGCTTCACATATGTATTGTTCTTTCTACCCTCCAGATGAGGATGAAGAAGAAGGTGATTGTGAAGAAG +AAGAGTTTGAGCCATCAACTCAATATGAGTATGGTACTGAAGATGATTACCAAGGTAAACCTTTGGAATT +TGGTGCCACTTCTGCTGCTCTTCAACCTGAAGAAGAGCAAGAAGAAGATTGGTTAGATGATGATAGTCAA +CAAACTGTTGGTCAACAAGACGGCAGTGAGGACAATCAGACAACTACTATTCAAACAATTGTTGAGGTTC +AACCTCAATTAGAGATGGAACTTACACCAGTTGTTCAGACTATTGAAGTGAATAGTTTTAGTGGTTATTT +AAAACTTACTGACAATGTATACATTAAAAATGCAGACATTGTGGAAGAAGCTAAAAAGGTAAAACCAACA +GTGGTTGTTAATGCAGCCAATGTTTACCTTAAACATGGAGGAGGTGTTGCAGGAGCCTTAAATAAGGCTA +CTAACAATGCCATGCAAGTTGAATCTGATGATTACATAGCTACTAATGGACCACTTAAAGTGGGTGGTAG +TTGTGTTTTAAGCGGACACAATCTTGCTAAACACTGTCTTCATGTTGTCGGCCCAAATGTTAACAAAGGT +GAAGACATTCAACTTCTTAAGAGTGCTTATGAAAATTTTAATCAGCACGAAGTTCTACTTGCACCATTAT +TATCAGCTGGTATTTTTGGTGCTGACCCTATACATTCTTTAAGAGTTTGTGTAGATACTGTTCGCACAAA +TGTCTACTTAGCTGTCTTTGATAAAAATCTCTATGACAAACTTGTTTCAAGCTTTTTGGAAATGAAGAGT +GAAAAGCAAGTTGAACAAAAGATCGCTGAGATTCCTAAAGAGGAAGTTAAGCCATTTATAACTGAAAGTA +AACCTTCAGTTGAACAGAGAAAACAAGATGATAAGAAAATCAAAGCTTGTGTTGAAGAAGTTACAACAAC +TCTGGAAGAAACTAAGTTCCTCACAGAAAACTTGTTACTTTATATTGACATTAATGGCAATCTTCATCCA +GATTCTGCCACTCTTGTTAGTGACATTGACATCACTTTCTTAAAGAAAGATGCTCCATATATAGTGGGTG +ATGTTGTTCAAGAGGGTGTTTTAACTGCTGTGGTTATACCTACTAAAAAGGCTGGTGGCACTACTGAAAT +GCTAGCGAAAGCTTTGAGAAAAGTGCCAACAGACAATTATATAACCACTTACCCGGGTCAGGGTTTAAAT +GGTTACACTGTAGAGGAGGCAAAGACAGTGCTTAAAAAGTGTAAAAGTGCCTTTTACATTCTACCATCTA +TTATCTCTAATGAGAAGCAAGAAATTCTTGGAACTGTTTCTTGGAATTTGCGAGAAATGCTTGCACATGC +AGAAGAAACACGCAAATTAATGCCTGTCTGTGTGGAAACTAAAGCCATAGTTTCAACTATACAGCGTAAA +TATAAGGGTATTAAAATACAAGAGGGTGTGGTTGATTATGGTGCTAGATTTTACTTTTACACCAGTAAAA +CAACTGTAGCGTCACTTATCAACACACTTAACGATCTAAATGAAACTCTTGTTACAATGCCACTTGGCTA +TGTAACACATGGCTTAAATTTGGAAGAAGCTGCTCGGTATATGAGATCTCTCAAAGTGCCAGCTACAGTT +TCTGTTTCTTCACCTGATGCTGTTACAGCGTATAATGGTTATCTTACTTCTTCTTCTAAAACACCTGAAG +AACATTTTATTGAAACCATCTCACTTGCTGGTTCCTATAAAGATTGGTCCTATTCTGGACAATCTACACA +ACTAGGTATAGAATTTCTTAAGAGAGGTGATAAAAGTGTATATTACACTAGTAATCCTACCACATTCCAC +CTAGATGGTGAAGTTATCACCTTTGACAATCTTAAGACACTTCTTTCTTTGAGAGAAGTGAGGACTATTA +AGGTGTTTACAACAGTAGACAACATTAACCTCCACACGCAAGTTGTGGACATGTCAATGACATATGGACA +ACAGTTTGGTCCAACTTATTTGGATGGAGCTGATGTTACTAAAATAAAACCTCATAATTCACATGAAGGT +AAAACATTTTATGTTTTACCTAATGATGACACTCTACGTGTTGAGGCTTTTGAGTACTACCACACAACTG +ATCCTAGTTTTCTGGGTAGGTACATGTCAGCATTAAATCACACTAAAAAGTGGAAATACCCACAAGTTAA +TGGTTTAACTTCTATTAAATGGGCAGATAACAACTGTTATCTTGCCACTGCATTGTTAACACTCCAACAA +ATAGAGTTGAAGTTTAATCCACCTGCTCTACAAGATGCTTATTACAGAGCAAGGGCTGGTGAAGCTGCTA +ACTTTTGTGCACTTATCTTAGCCTACTGTAATAAGACAGTAGGTGAGTTAGGTGATGTTAGAGAAACAAT +GAGTTACTTGTTTCAACATGCCAATTTAGATTCTTGCAAAAGAGTCTTGAACGTGGTGTGTAAAACTTGT +GGACAACAGCAGACAACCCTTAAGGGTGTAGAAGCTGTTATGTACATGGGCACACTTTCTTATGAACAAT +TTAAGAAAGGTGTTCAGATACCTTGTACGTGTGGTAAACAAGCTACAAAATATCTAGTACAACAGGAGTC +ACCTTTTGTTATGATGTCAGCACCACCTGCTCAGTATGAACTTAAGCATGGTACATTTACTTGTGCTAGT +GAGTACACTGGTAATTACCAGTGTGGTCACTATAAACATATAACTTCTAAAGAAACTTTGTATTGCATAG +ACGGTGCTTTACTTACAAAGTCCTCAGAATACAAAGGTCCTATTACGGATGTTTTCTACAAAGAAAACAG +TTACACAACAACCATAAAACCAGTTACTTATAAATTGGATGGTGTTGTTTGTACAGAAATTGACCCTAAG +TTGGACAATTATTATAAGAAAGACAATTCTTATTTCACAGAGCAACCAATTGATCTTGTACCAAACCAAC +CATATCCAAACGCAAGCTTCGATAATTTTAAGTTTGTATGTGATAATATCAAATTTGCTGATGATTTAAA +CCAGTTAACTGGTTATAAGAAACCTGCTTCAAGAGAGCTTAAAGTTACATTTTTCCCTGACTTAAATGGT +GATGTGGTGGCTATTGATTATAAACACTACACACCCTCTTTTAAGAAAGGAGCTAAATTGTTACATAAAC +CTATTGTTTGGCATGTTAACAATGCAACTAATAAAGCCACGTATAAACCAAATACCTGGTGTATACGTTG +TCTTTGGAGCACAAAACCAGTTGAAACATCAAATTCGTTTGATGTACTGAAGTCAGAGGACGCGCAGGGA +ATGGATAATCTTGCCTGCGAAGATCTAAAACCAGTCTCTGAAGAAGTAGTGGAAAATCCTACCATACAGA +AAGACGTTCTTGAGTGTAATGTGAAAACTACCGAAGTTGTAGGAGACATTATACTTAAACCAGCAAATAA +TAGTTTAAAAATTACAGAAGAGGTTGGCCACACAGATCTAATGGCTGCTTATGTAGACAATTCTAGTCTT +ACTATTAAGAAACCTAATGAATTATCTAGAGTATTAGGTTTGAAAACCCTTGCTACTCATGGTTTAGCTG +CTGTTAATAGTGTCCCTTGGGATACTATAGCTAATTATGCTAAGCCTTTTCTTAACAAAGTTGTTAGTAC +AACTACTAACATAGTTACACGGTGTTTAAACCGTGTTTGTACTAATTATATGCCTTATTTCTTTACTTTA +TTGCTACAATTGTGTACTTTTACTAGAAGTACAAATTCTAGAATTAAAGCATCTATGCCGACTACTATAG +CAAAGAATACTGTTAAGAGTGTCGGTAAATTTTGTCTAGAGGCTTCATTTAATTATTTGAAGTCACCTAA +TTTTTCTAAACTGATAAATATTATAATTTGGTTTTTACTATTAAGTGTTTGCCTAGGTTCTTTAATCTAC +TCAACCGCTGCTTTAGGTGTTTTAATGTCTAATTTAGGCATGCCTTCTTACTGTACTGGTTACAGAGAAG +GCTATTTGAACTCTACTAATGTCACTATTGCAACCTACTGTACTGGTTCTATACCTTGTAGTGTTTGTCT +TAGTGGTTTAGATTCTTTAGACACCTATCCTTCTTTAGAAACTATACAAATTACCATTTCATCTTTTAAA +TGGGATTTAACTGCTTTTGGCTTAGTTGCAGAGTGGTTTTTGGCATATATTCTTTTCACTAGGTTTTTCT +ATGTACTTGGATTGGCTGCAATCATGCAATTGTTTTTCAGCTATTTTGCAGTACATTTTATTAGTAATTC +TTGGCTTATGTGGTTAATAATTAATCTTGTACAAATGGCCCCGATTTCAGCTATGGTTAGAATGTACATC +TTCTTTGCATCATTTTATTATGTATGGAAAAGTTATGTGCATGTTGTAGACGGTTGTAATTCATCAACTT +GTATGATGTGTTACAAACGTAATAGAGCAACAAGAGTCGAATGTACAACTATTGTTAATGGTGTTAGAAG +GTCCTTTTATGTCTATGCTAATGGAGGTAAAGGCTTTTGCAAACTACACAATTGGAATTGTGTTAATTGT +GATACATTCTGTGCTGGTAGTACATTTATTAGTGATGAAGTTGCGAGAGACTTGTCACTACAGTTTAAAA +GACCAATAAATCCTACTGACCAGTCTTCTTACATCGTTGATAGTGTTACAGTGAAGAATGGTTCCATCCA +TCTTTACTTTGATAAAGCTGGTCAAAAGACTTATGAAAGACATTCTCTCTCTCATTTTGTTAACTTAGAC +AACCTGAGAGCTAATAACACTAAAGGTTCATTGCCTATTAATGTTATAGTTTTTGATGGTAAATCAAAAT +GTGAAGAATCATCTGCAAAATCAGCGTCTGTTTACTACAGTCAGCTTATGTGTCAACCTATACTGTTACT +AGATCAGGCATTAGTGTCTGATGTTGGTGATAGTGCGGAAGTTGCAGTTAAAATGTTTGATGCTTACGTT +AATACGTTTTCATCAACTTTTAACGTACCAATGGAAAAACTCAAAACACTAGTTGCAACTGCAGAAGCTG +AACTTGCAAAGAATGTGTCCTTAGACAATGTCTTATCTACTTTTATTTCAGCAGCTCGGCAAGGGTTTGT +TGATTCAGATGTAGAAACTAAAGATGTTGTTGAATGTCTTAAATTGTCACATCAATCTGACATAGAAGTT +ACTGGCGATAGTTGTAATAACTATATGCTCACCTATAACAAAGTTGAAAACATGACACCCCGTGACCTTG +GTGCTTGTATTGACTGTAGTGCGCGTCATATTAATGCGCAGGTAGCAAAAAGTCACAACATTGCTTTGAT +ATGGAACGTTAAAGATTTCATGTCATTGTCTGAACAACTACGAAAACAAATACGTAGTGCTGCTAAAAAG +AATAACTTACCTTTTAAGTTGACATGTGCAACTACTAGACAAGTTGTTAATGTTGTAACAACAAAGATAG +CACTTAAGGGTGGTAAAATTGTTAATAATTGGTTGAAGCAGTTAATTAAAGTTACACTTGTGTTCCTTTT +TGTTGCTGCTATTTTCTATTTAATAACACCTGTTCATGTCATGTCTAAACATACTGACTTTTCAAGTGAA +ATCATAGGATACAAGGCTATTGATGGTGGTGTCACTCGTGACATAGCATCTACAGATACTTGTTTTGCTA +ACAAACATGCTGATTTTGACACATGGTTTAGCCAGCGTGGTGGTAGTTATACTAATGACAAAGCTTGCCC +ATTGATTGCTGCAGTCATAACAAGAGAAGTGGGTTTTGTCGTGCCTGGTTTGCCTGGCACGATATTACGC +ACAACTAATGGTGACTTTTTGCATTTCTTACCTAGAGTTTTTAGTGCAGTTGGTAACATCTGTTACACAC +CATCAAAACTTATAGAGTACACTGACTTTGCAACATCAGCTTGTGTTTTGGCTGCTGAATGTACAATTTT +TAAAGATGCTTCTGGTAAGCCAGTACCATATTGTTATGATACCAATGTACTAGAAGGTTCTGTTGCTTAT +GAAAGTTTACGCCCTGACACACGTTATGTGCTCATGGATGGCTCTATTATTCAATTTCCTAACACCTACC +TTGAAGGTTCTGTTAGAGTGGTAACAACTTTTGATTCTGAGTACTGTAGGCACGGCACTTGTGAAAGATC +AGAAGCTGGTGTTTGTGTATCTACTAGTGGTAGATGGGTACTTAACAATGATTATTACAGATCTTTACCA +GGAGTTTTCTGTGGTGTAGATGCTGTAAATTTACTTACTAATATGTTTACACCACTAATTCAACCTATTG +GTGCTTTGGACATATCAGCATCTATAGTAGCTGGTGGTATTGTAGCTATCGTAGTAACATGCCTTGCCTA +CTATTTTATGAGGTTTAGAAGAGCTTTTGGTGAATACAGTCATGTAGTTGCCTTTAATACTTTACTATTC +CTTATGTCATTCACTGTACTCTGTTTAACACCAGTTTACTCATTCTTACCTGGTGTTTATTCTGTTATTT +ACTTGTACTTGACATTTTATCTTACTAATGATGTTTCTTTTTTAGCACATATTCAGTGGATGGTTATGTT +CACACCTTTAGTACCTTTCTGGATAACAATTGCTTATATCATTTGTATTTCCACAAAGCATTTCTATTGG +TTCTTTAGTAATTACCTAAAGAGACGTGTAGTCTTTAATGGTGTTTCCTTTAGTACTTTTGAAGAAGCTG +CGCTGTGCACCTTTTTGTTAAATAAAGAAATGTATCTAAAGTTGCGTAGTGATGTGCTATTACCTCTTAC +GCAATATAATAGATACTTAGCTCTTTATAATAAGTACAAGTATTTTAGTGGAGCAATGGATACAACTAGC +TACAGAGAAGCTGCTTGTTGTCATCTCGCAAAGGCTCTCAATGACTTCAGTAACTCAGGTTCTGATGTTC +TTTACCAACCACCACAAACCTCTATCACCTCAGCTGTTTTGCAGAGTGGTTTTAGAAAAATGGCATTCCC +ATCTGGTAAAGTTGAGGGTTGTATGGTACAAGTAACTTGTGGTACAACTACACTTAACGGTCTTTGGCTT +GATGACGTAGTTTACTGTCCAAGACATGTGATCTGCACCTCTGAAGACATGCTTAACCCTAATTATGAAG +ATTTACTCATTCGTAAGTCTAATCATAATTTCTTGGTACAGGCTGGTAATGTTCAACTCAGGGTTATTGG +ACATTCTATGCAAAATTGTGTACTTAAGCTTAAGGTTGATACAGCCAATCCTAAGACACCTAAGTATAAG +TTTGTTCGCATTCAACCAGGACAGACTTTTTCAGTGTTAGCTTGTTACAATGGTTCACCATCTGGTGTTT +ACCAATGTGCTATGAGGCCCAATTTCACTATTAAGGGTTCATTCCTTAATGGTTCATGTGGTAGTGTTGG +TTTTAACATAGATTATGACTGTGTCTCTTTTTGTTACATGCACCATATGGAATTACCAACTGGAGTTCAT +GCTGGCACAGACTTAGAAGGTAACTTTTATGGACCTTTTGTTGACAGGCAAACAGCACAAGCAGCTGGTA +CGGACACAACTATTACAGTTAATGTTTTAGCTTGGTTGTACGCTGCTGTTATAAATGGAGACAGGTGGTT +TCTCAATCGATTTACCACAACTCTTAATGACTTTAACCTTGTGGCTATGAAGTACAATTATGAACCTCTA +ACACAAGACCATGTTGACATACTAGGACCTCTTTCTGCTCAAACTGGAATTGCCGTTTTAGATATGTGTG +CTTCATTAAAAGAATTACTGCAAAATGGTATGAATGGACGTACCATATTGGGTAGTGCTTTATTAGAAGA +TGAATTTACACCTTTTGATGTTGTTAGACAATGCTCAGGTGTTACTTTCCAAAGTGCAGTGAAAAGAACA +ATCAAGGGTACACACCACTGGTTGTTACTCACAATTTTGACTTCACTTTTAGTTTTAGTCCAGAGTACTC +AATGGTCTTTGTTCTTTTTTTTGTATGAAAATGCCTTTTTACCTTTTGCTATGGGTATTATTGCTATGTC +TGCTTTTGCAATGATGTTTGTCAAACATAAGCATGCATTTCTCTGTTTGTTTTTGTTACCTTCTCTTGCC +ACTGTAGCTTATTTTAATATGGTCTATATGCCTGCTAGTTGGGTGATGCGTATTATGACATGGTTGGATA +TGGTTGATACTAGTTTGTCTGGTTTTAAGCTAAAAGACTGTGTTATGTATGCATCAGCTGTAGTGTTACT +AATCCTTATGACAGCAAGAACTGTGTATGATGATGGTGCTAGGAGAGTGTGGACACTTATGAATGTCTTG +ACACTCGTTTATAAAGTTTATTATGGTAATGCTTTAGATCAAGCCATTTCCATGTGGGCTCTTATAATCT +CTGTTACTTCTAACTACTCAGGTGTAGTTACAACTGTCATGTTTTTGGCCAGAGGTATTGTTTTTATGTG +TGTTGAGTATTGCCCTATTTTCTTCATAACTGGTAATACACTTCAGTGTATAATGCTAGTTTATTGTTTC +TTAGGCTATTTTTGTACTTGTTACTTTGGCCTCTTTTGTTTACTCAACCGCTACTTTAGACTGACTCTTG +GTGTTTATGATTACTTAGTTTCTACACAGGAGTTTAGATATATGAATTCACAGGGACTACTCCCACCCAA +GAATAGCATAGATGCCTTCAAACTCAACATTAAATTGTTGGGTGTTGGTGGCAAACCTTGTATCAAAGTA +GCCACTGTACAGTCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAAC +TCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAA +AGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTA +GACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAAGCTATAGCCTCAGAGTTTA +GTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGA +TTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCA +GCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTG +AGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAA +TGATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACA +ACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACAT +TTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAG +TGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCT +GCTGTCAAATTACAGAATAATGAGCTTAGTCCTGTTGCACTACGACAGATGTCTTGTGCTGCCGGTACTA +CACAAACTGCTTGCACTGATGACAATGCGTTAGCTTACTACAACACAACAAAGGGAGGTAGGTTTGTACT +TGCACTGTTATCCGATTTACAGGATTTGAAATGGGCTAGATTCCCTAAGAGTGATGGAACTGGTACTATC +TATACAGAACTGGAACCACCTTGTAGGTTTGTTACAGACACACCTAAAGGTCCTAAAGTGAAGTATTTAT +ACTTTATTAAAGGATTAAACAACCTAAATAGAGGTATGGTACTTGGTAGTTTAGCTGCCACAGTACGTCT +ACAAGCTGGTAATGCAACAGAAGTGCCTGCCAATTCAACTGTATTATCTTTCTGTGCTTTTGCTGTAGAT +GCTGCTAAAGCTTACAAAGATTATCTAGCTAGTGGGGGACAACCAATCACTAATTGTGTTAAGATGTTGT +GTACACACACTGGTACTGGTCAGGCAATAACAGTTACACCGGAAGCCAATATGGATCAAGAATCCTTTGG +TGGTGCATCGTGTTGTCTGTACTGCCGTTGCCACATAGATCATCCAAATCCTAAAGGATTTTGTGACTTA +AAAGGTAAGTATGTACAAATACCTACAACTTGTGCTAATGACCCTGTGGGTTTTACACTTAAAAACACAG +TCTGTACCGTCTGCGGTATGTGGAAAGGTTATGGCTGTAGTTGTGATCAACTCCGCGAACCCATGCTTCA +GTCAGCTGATGCACAATCGTTTTTAAACGGGTTTGCGGTGTAAGTGCAGCCCGTCTTACACCGTGCGGCA +CAGGCACTAGTACTGATGTCGTATACAGGGCTTTTGACATCTACAATGATAAAGTAGCTGGTTTTGCTAA +ATTCCTAAAAACTAATTGTTGTCGCTTCCAAGAAAAGGACGAAGATGACAATTTAATTGATTCTTACTTT +GTAGTTAAGAGACACACTTTCTCTAACTACCAACATGAAGAAACAATTTATAATTTACTTAAGGATTGTC +CAGCTGTTGCTAAACATGACTTCTTTAAGTTTAGAATAGACGGTGACATGGTACCACATATATCACGTCA +ACGTCTTACTAAATACACAATGGCAGACCTCGTCTATGCTTTAAGGCATTTTGATGAAGGTAATTGTGAC +ACATTAAAAGAAATACTTGTCACATACAATTGTTGTGATGATGATTATTTCAATAAAAAGGACTGGTATG +ATTTTGTAGAAAACCCAGATATATTACGCGTATACGCCAACTTAGGTGAACGTGTACGCCAAGCTTTGTT +AAAAACAGTACAATTCTGTGATGCCATGCGAAATGCTGGTATTGTTGGTGTACTGACATTAGATAATCAA +GATCTCAATGGTAACTGGTATGATTTCGGTGATTTCATACAAACCACGCCAGGTAGTGGAGTTCCTGTTG +TAGATTCTTATTATTCATTGTTAATGCCTATATTAACCTTGACCAGGGCTTTAACTGCAGAGTCACATGT +TGACACTGACTTAACAAAGCCTTACATTAAGTGGGATTTGTTAAAATATGACTTCACGGAAGAGAGGTTA +AAACTCTTTGACCGTTATTTTAAATATTGGGATCAGACATACCACCCAAATTGTGTTAACTGTTTGGATG +ACAGATGCATTCTGCATTGTGCAAACTTTAATGTTTTATTCTCTACAGTGTTCCCACCTACAAGTTTTGG +ACCACTAGTGAGAAAAATATTTGTTGATGGTGTTCCATTTGTAGTTTCAACTGGATACCACTTCAGAGAG +CTAGGTGTTGTACATAATCAGGATGTAAACTTACATAGCTCTAGACTTAGTTTTAAGGAATTACTTGTGT +ATGCTGCTGACCCTGCTATGCACGCTGCTTCTGGTAATCTATTACTAGATAAACGCACTACGTGCTTTTC +AGTAGCTGCACTTACTAACAATGTTGCTTTTCAAACTGTCAAACCCGGTAATTTTAACAAAGACTTCTAT +GACTTTGCTGTGTCTAAGGGTTTCTTTAAGGAAGGAAGTTCTGTTGAATTAAAACACTTCTTCTTTGCTC +AGGATGGTAATGCTGCTATCAGCGATTATGACTACTATCGTTATAATCTACCAACAATGTGTGATATCAG +ACAACTACTATTTGTAGTTGAAGTTGTTGATAAGTACTTTGATTGTTACGATGGTGGCTGTATTAATGCT +AACCAAGTCATCGTCAACAACCTAGACAAATCAGCTGGTTTTCCATTTAATAAATGGGGTAAGGCTAGAC +TTTATTATGATTCAATGAGTTATGAGGATCAAGATGCACTTTTCGCATATACAAAACGTAATGTCATCCC +TACTATAACTCAAATGAATCTTAAGTATGCCATTAGTGCAAAGAATAGAGCTCGCACCGTAGCTGGTGTC +TCTATCTGTAGTACTATGACCAATAGACAGTTTCATCAAAAATTATTGAAATCAATAGCCGCCACTAGAG +GAGCTACTGTAGTAATTGGAACAAGCAAATTCTATGGTGGTTGGCACAACATGTTAAAAACTGTTTATAG +TGATGTAGAAAACCCTCACCTTATGGGTTGGGATTATCCTAAATGTGATAGAGCCATGCCTAACATGCTT +AGAATTATGGCCTCACTTGTTCTTGCTCGCAAACATACAACGTGTTGTAGCTTGTCACACCGTTTCTATA +GATTAGCTAATGAGTGTGCTCAAGTATTGAGTGAAATGGTCATGTGTGGCGGTTCACTATATGTTAAACC +AGGTGGAACCTCATCAGGAGATGCCACAACTGCTTATGCTAATAGTGTTTTTAACATTTGTCAAGCTGTC +ACGGCCAATGTTAATGCACTTTTATCTACTGATGGTAACAAAATTGCCGATAAGTATGTCCGCAATTTAC +AACACAGACTTTATGAGTGTCTCTATAGAAATAGAGATGTTGACACAGACTTTGTGAATGAGTTTTACGC +ATATTTGCGTAAACATTTCTCAATGATGATACTCTCTGACGATGCTGTTGTGTGTTTCAATAGCACTTAT +GCATCTCAAGGTCTAGTGGCTAGCATAAAGAACTTTAAGTCAGTTCTTTATTATCAAAACAATGTTTTTA +TGTCTGAAGCAAAATGTTGGACTGAGACTGACCTTACTAAAGGACCTCATGAATTTTGCTCTCAACATAC +AATGCTAGTTAAACAGGGTGATGATTATGTGTACCTTCCTTACCCAGATCCATCAAGAATCCTAGGGGCC +GGCTGTTTTGTAGATGATATCGTAAAAACAGATGGTACACTTATGATTGAACGGTTCGTGTCTTTAGCTA +TAGATGCTTACCCACTTACTAAACATCCTAATCAGGAGTATGCTGATGTCTTTCATTTGTACTTACAATA +CATAAGAAAGCTACATGATGAGTTAACAGGACACATGTTAGACATGTATTCTGTTATGCTTACTAATGAT +AACACTTCAAGGTATTGGGAACCTGAGTTTTATGAGGCTATGTACACACCGCATACAGTCTTACAGGCTG +TTGGGGCTTGTGTTCTTTGCAATTCACAGACTTCATTAAGATGTGGTGCTTGCATACGTAGACCATTCTT +ATGTTGTAAATGCTGTTACGACCATGTCATATCAACATCACATAAATTAGTCTTGTCTGTTAATCCGTAT +GTTTGCAATGCTCCAGGTTGTGATGTCACAGATGTGACTCAACTTTACTTAGGAGGTATGAGCTATTATT +GTAAATCACATAAACCACCCATTAGTTTTCCATTGTGTGCTAATGGACAAGTTTTTGGTTTATATAAAAA +TACATGTGTTGGTAGCGATAATGTTACTGACTTTAATGCAATTGCAACATGTGACTGGACAAATGCTGGT +GATTACATTTTAGCTAACACCTGTACTGAAAGACTCAAGCTTTTTGCAGCAGAAACGCTCAAAGCTACTG +AGGAGACATTTAAACTGTCTTATGGTATTGCTACTGTACGTGAAGTGCTGTCTGACAGAGAATTACATCT +TTCATGGGAAGTTGGTAAACCTAGACCACCACTTAACCGAAATTATGTCTTTACTGGTTATCGTGTAACT +AAAAACAGTAAAGTACAAATAGGAGAGTACACCTTTGAAAAAGGTGACTATGGTGATGCTGTTGTTTACC +GAGGTACAACAACTTACAAATTAAATGTTGGTGATTATTTTGTGCTGACATCACATACAGTAATGCCATT +AAGTGCACCTACACTAGTGCCACAAGAGCACTATGTTAGAATTACTGGCTTATACCCAACACTCAATATC +TCAGATGAGTTTTCTAGCAATGTTGCAAATTATCAAAAGGTTGGTATGCAAAAGTATTCTACACTCCAGG +GACCACCTGGTACTGGTAAGAGTCATTTTGCTATTGGCCTAGCTCTCTACTACCCTTCTGCTCGCATAGT +GTATACAGCTTGCTCTCATGCCGCTGTTGATGCACTATGTGAGAAGGCATTAAAATATTTGCCTATAGAT +AAATGTAGTAGAATTATACCTGCACGTGCTCGTGTAGAGTGTTTTGATAAATTCAAAGTGAATTCAACAT +TAGAACAGTATGTCTTTTGTACTGTAAATGCATTGCCTGAGACGACAGCAGATATAGTTGTCTTTGATGA +AATTTCAATGGCCACAAATTATGATTTGAGTGTTGTCAATGCCAGATTACGTGCTAAGCACTATGTGTAC +ATTGGCGACCCTGCTCAATTACCTGCACCACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATT +TCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCC +TGCTGAAATTGTTGACACTGTGAGTGCTTTGGTTTATGATAATAAGCTTAAAGCACATAAAGACAAATCA +GCTCAATGCTTTAAAATGTTTTATAAGGGTGTTATCACGCATGATGTTTCATCTGCAATTAACAGGCCAC +AAATAGGCGTGGTAAGAGAATTCCTTACACGTAACCCTGCTTGGAGAAAAGCTGTCTTTATTTCACCTTA +TAATTCACAGAATGCTGTAGCCTCAAAGATTTTGGGACTACCAACTCAAACTGTTGATTCATCACAGGGC +TCAGAATATGACTATGTCATATTCACTCAAACCACTGAAACAGCTCACTCTTGTAATGTAAACAGATTTA +ATGTTGCTATTACCAGAGCAAAAGTAGGCATACTTTGCATAATGTCTGATAGAGACCTTTATGACAAGTT +GCAATTTACAAGTCTTGAAATTCCACGTAGGAATGTGGCAACTTTACAAGCTGAAAATGTAACAGGACTC +TTTAAAGATTGTAGTAAGGTAATCACTGGGTTACATCCTACACAGGCACCTACACACCTCAGTGTTGACA +CTAAATTCAAAACTGAAGGTTTATGTGTTGACATACCTGGCATACCTAAGGACATGACCTATAGAAGACT +CATCTCTATGATGGGTTTTAAAATGAATTATCAAGTTAATGGTTACCCTAACATGTTTATCACCCGCGAA +GAAGCTATAAGACATGTACGTGCATGGATTGGCTTCGATGTCGAGGGGTGTCATGCTACTAGAGAAGCTG +TTGGTACCAATTTACCTTTACAGCTAGGTTTTTCTACAGGTGTTAACCTAGTTGCTGTACCTACAGGTTA +TGTTGATACACCTAATAATACAGATTTTTCCAGAGTTAGTGCTAAACCACCGCCTGGAGATCAATTTAAA +CACCTCATACCACTTATGTACAAAGGACTTCCTTGGAATGTAGTGCGTATAAAGATTGTACAAATGTTAA +GTGACACACTTAAAAATCTCTCTGACAGAGTCGTATTTGTCTTATGGGCACATGGCTTTGAGTTGACATC +TATGAAGTATTTTGTGAAAATAGGACCTGAGCGCACCTGTTGTCTATGTGATAGACGTGCCACATGCTTT +TCCACTGCTTCAGACACTTATGCCTGTTGGCATCATTCTATTGGATTTGATTACGTCTATAATCCGTTTA +TGATTGATGTTCAACAATGGGGTTTTACAGGTAACCTACAAAGCAACCATGATCTGTATTGTCAAGTCCA +TGGTAATGCACATGTAGCTAGTTGTGATGCAATCATGACTAGGTGTCTAGCTGTCCACGAGTGCTTTGTT +AAGCGTGTTGACTGGACTATTGAATATCCTATAATTGGTGATGAACTGAAGATTAATGCGGCTTGTAGAA +AGGTTCAACACATGGTTGTTAAAGCTGCATTATTAGCAGACAAATTCCCAGTTCTTCACGACATTGGTAA +CCCTAAAGCTATTAAGTGTGTACCTCAAGCTGATGTAGAATGGAAGTTCTATGATGCACAGCCTTGTAGT +GACAAAGCTTATAAAATAGAAGAATTATTCTATTCTTATGCCACACATTCTGACAAATTCACAGATGGTG +TATGCCTATTTTGGAATTGCAATGTCGATAGATATCCTGCTAATTCCATTGTTTGTAGATTTGACACTAG +AGTGCTATCTAACCTTAACTTGCCTGGTTGTGATGGTGGCAGTTTGTATGTAAATAAACATGCATTCCAC +ACACCAGCTTTTGATAAAAGTGCTTTTGTTAATTTAAAACAATTACCATTTTTCTATTACTCTGACAGTC +CATGTGAGTCTCATGGAAAACAAGTAGTGTCAGATATAGATTATGTACCACTAAAGTCTGCTACGTGTAT +AACACGTTGCAATTTAGGTGGTGCTGTCTGTAGACATCATGCTAATGAGTACAGATTGTATCTCGATGCT +TATAACATGATGATCTCAGCTGGCTTTAGCTTGTGGGTTTACAAACAATTTGATACTTATAACCTCTGGA +ACACTTTTACAAGACTTCAGAGTTTAGAAAATGTGGCTTTTAATGTTGTAAATAAGGGACACTTTGATGG +ACAACAGGGTGAAGTACCAGTTTCTATCATTAATAACACTGTTTACACAAAAGTTGATGGTGTTGATGTA +GAATTGTTTGAAAATAAAACAACATTACCTGTTAATGTAGCATTTGAGCTTTGGGCTAAGCGCAACATTA +AACCAGTACCAGAGGTGAAAATACTCAATAATTTGGGTGTGGACATTGCTGCTAATACTGTGATCTGGGA +CTACAAAAGAGATGCTCCAGCACATATATCTACTATTGGTGTTTGTTCTATGACTGACATAGCCAAGAAA +CCAACTGAAACGATTTGTGCACCACTCACTGTCTTTTTTGATGGTAGAGTTGATGGTCAAGTAGACTTAT +TTAGAAATGCCCGTAATGGTGTTCTTATTACAGAAGGTAGTGTTAAAGGTTTACAACCATCTGTAGGTCC +CAAACAAGCTAGTCTTAATGGAGTCACATTAATTGGAGAAGCCGTAAAAACACAGTTCAATTATTATAAG +AAAGTTGATGGTGTTGTCCAACAATTACCTGAAACTTACTTTACTCAGAGTAGAAATTTACAAGAATTTA +AACCCAGGAGTCAAATGGAAATTGATTTCTTAGAATTAGCTATGGATGAATTCATTGAACGGTATAAATT +AGAAGGCTATGCCTTCGAACATATCGTTTATGGAGATTTTAGTCATAGTCAGTTAGGTGGTTTACATCTA +CTGATTGGACTAGCTAAACGTTTTAAGGAATCACCTTTTGAATTAGAAGATTTTATTCCTATGGACAGTA +CAGTTAAAAACTATTTCATAACAGATGCGCAAACAGGTTCATCTAAGTGTGTGTGTTCTGTTATTGATTT +ATTACTTGATGATTTTGTTGAAATAATAAAATCCCAAGATTTATCTGTAGTTTCTAAGGTTGTCAAAGTG +ACTATTGACTATACAGAAATTTCATTTATGCTTTGGTGTAAAGATGGCCATGTAGAAACATTTTACCCAA +AATTACAATCTAGTCAAGCGTGGCAACCGGGTGTTGCTATGCCTAATCTTTACAAAATGCAAAGAATGCT +ATTAGAAAAGTGTGACCTTCAAAATTATGGTGATAGTGCAACATTACCTAAAGGCATAATGATGAATGTC +GCAAAATATACTCAACTGTGTCAATATTTAAACACATTAACATTAGCTGTACCCTATAATATGAGAGTTA +TACATTTTGGTGCTGGTTCTGATAAAGGAGTTGCACCAGGTACAGCTGTTTTAAGACAGTGGTTGCCTAC +GGGTACGCTGCTTGTCGATTCAGATCTTAATGACTTTGTCTCTGATGCAGATTCAACTTTGATTGGTGAT +TGTGCAACTGTACATACAGCTAATAAATGGGATCTCATTATTAGTGATATGTACGACCCTAAGACTAAAA +ATGTTACAAAAGAAAATGACTCTAAAGAGGGTTTTTTCACTTACATTTGTGGGTTTATACAACAAAAGCT +AGCTCTTGGAGGTTCCGTGGCTATAAAGATAACAGAACATTCTTGGAATGCTGATCTTTATAAGCTCATG +GGACACTTCGCATGGTGGACAGCCTTTGTTACTAATGTGAATGCGTCATCATCTGAAGCATTTTTAATTG +GATGTAATTATCTTGGCAAACCACGCGAACAAATAGATGGTTATGTCATGCATGCAAATTACATATTTTG +GAGGAATACAAATCCAATTCAGTTGTCTTCCTATTCTTTATTTGACATGAGTAAATTTCCCCTTAAATTA +AGGGGTACTGCTGTTATGTCTTTAAAAGAAGGTCAAATCAATGATATGATTTTATCTCTTCTTAGTAAAG +GTAGACTTATAATTAGAGAAAACAACAGAGTTGTTATTTCTAGTGATGTTCTTGTTAACAACTAAACGAA +CAATGTTTGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACCAGAACTCA +ATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGACAAAGTTTTCAGATCCTCA +GTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCCAATGTTACTTGGTTCCATGCTATACATG +TCTCTGGGACCAATGGTACTAAGAGGTTTGATAACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGC +TTCCACTGAGAAGTCTAACATAATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCC +CTACTTATTGTTAATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATGATCCAT +TTTTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTATTCTAGTGC +GAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAAGGAAAACAGGGTAATTTC +AAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTATTTTAAAATATATTCTAAGCACACGCCTA +TTAATTTAGTGCGTGATCTCCCTCAGGGTTTTTCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTAT +TAACATCACTAGGTTTCAAACTTTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCA +GGTTGGACAGCTGGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATA +ATGAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAGTGTACGTT +GAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTCCAACCAACAGAATCTATT +GTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAAGTTTTTAACGCCACCAGATTTGCATCTG +TTTATGCTTGGAACAGGAAGAGAATCAGCAACTGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATC +ATTTTCCACTTTTAAGTGTTATGGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTAT +GCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTG +ATTATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAATCTTGATTC +TAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAATCTCAAACCTTTTGAGAGA +GATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGTAATGGTGTTGAAGGTTTTAATTGTTACT +TTCCTTTACAATCATATGGTTTCCAACCCACTAATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACT +TTCTTTTGAACTTCTACATGCACCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAAC +AAATGTGTCAATTTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTC +TGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAGACACTTGA +GATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCAGGAACAAATACTTCTAAC +CAGGTTGCTGTTCTTTATCAGGATGTTAACTGCACAGAAGTCCCTGTTGCTATTCATGCAGATCAACTTA +CTCCTACTTGGCGTGTTTATTCTACAGGTTCTAATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGC +TGAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACT +CAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTG +GTGCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATTAGTGTTAC +CACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATGTACATTTGTGGTGATTCA +ACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGTACACAATTAAACCGTGCTTTAACTGGAA +TAGCTGTTGAACAAGACAAAAACACCCAAGAAGTTTTTGCACAAGTCAAACAAATTTACAAAACACCACC +AATTAAAGATTTTGGTGGTTTTAATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCA +TTTATTGAAGATCTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATT +GCCTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTTTTGCCACC +TTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGTACAATCACTTCTGGTTGG +ACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATGCAAATGGCTTATAGGTTTAATGGTATTG +GAGTTACACAGAATGTTCTCTATGAGAACCAAAAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAA +AATTCAAGACTCACTTTCTTCCACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCA +CAAGCTTTAAACACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATA +TCCTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGACTTCAAAG +TTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCTTCTGCTAATCTTGCTGCT +ACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTTGATTTTTGTGGAAAGGGCTATCATCTTA +TGTCCTTCCCTCAGTCAGCACCTCATGGTGTAGTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAA +GAACTTCACAACTGCTCCTGCCATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTT +TCAAATGGCACACACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACA +CATTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCTTTGCAACC +TGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACATCACCAGATGTTGATTTA +GGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAAAAAGAAATTGACCGCCTCAATGAGGTTG +CCAAGAATTTAAATGAATCTCTCATCGATCTCCAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCC +ATGGTACATTTGGCTAGGTTTTATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGT +ATGACCAGTTGCTGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACG +ACTCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACATAAACGAACTTATGGATTTGTTTATGAGA +ATCTTCACAATTGGAACTGTAACTTTGAAGCAAGGTGAAATCAAGGATGCTACTCCTTCAGATTTTGTTC +GCGCTACTGCAACGATACCGATACAAGCCTCACTCCCTTTCGGATGGCTTATTGTTGGCGTTGCACTTCT +TGCTGTTTTTCAGAGCGCTTCCAAAATCATAACCCTCAAAAAGAGATGGCAACTAGCACTCTCCAAGGGT +GTTCACTTTGTTTGCAACTTGCTGTTGTTGTTTGTAACAGTTTACTCACACCTTTTGCTCGTTGCTGCTG +GCCTTGAAGCCCCTTTTCTCTATCTTTATGCTTTAGTCTACTTCTTGCAGAGTATAAACTTTGTAAGAAT +AATAATGAGGCTTTGGCTTTGCTGGAAATGCCGTTCCAAAAACCCATTACTTTATGATGCCAACTATTTT +CTTTGCTGGCATACTAATTGTTACGACTATTGTATACCTTACAATAGTGTAACTTCTTCAATTGTCATTA +CTTCAGGTGATGGCACAACAAGTCCTATTTCTGAACATGACTACCAGATTGGTGGTTATACTGAAAAATG +GGAATCTGGAGTAAAAGACTGTGTTGTATTACACAGTTACTTCACTTCAGACTATTACCAGCTGTACTCA +ACTCAATTGAGTACAGACACTGGTGTTGAACATGTTACCTTCTTCATCTACAATAAAATTGTTGATGAGC +CTGAAGAACATGTCCAAATTCACACAATCGACGGTTCATCCGGAGTTGTTAATCCAGTAATGGAACCAAT +TTATGATGAACCGACGACGACTACTAGCGTGCCTTTGTAAGCACAAGCTGATGAGTACGAACTTATGTAC +TCATTCGTTTCGGAAGAGACAGGTACGTTAATAGTTAATAGCGTACTTCTTTTTCTTGCTTTCGTGGTAT +TCTTGCTAGTTACACTAGCCATCCTTACTGCGCTTCGATTGTGTGCGTACTGCTGCAATATTGTTAACGT +GAGTCTTGTAAAACCTTCTTTTTACGTTTACTCTCGTGTTAAAAATCTGAATTCTTCTAGAGTTCCTGAT +CTTCTGGTCTAAACGAACTAAATATTATATTAGTTTTTCTGTTTGGAACTTTAATTTTAGCCATGGCAGA +TTCCAACGGTACTATTACCGTTGAAGAGCTTAAAAAGCTCCTTGAACAATGGAACCTAGTAATAGGTTTC +CTATTCCTTACATGGATTTGTCTTCTACAATTTGCCTATGCCAACAGGAATAGGTTTTTGTATATAATTA +AGTTAATTTTCCTCTGGCTGTTATGGCCAGTAACTTTAGCTTGTTTTGTGCTTGCTGCTGTTTACAGAAT +AAATTGGATCACCGGTGGAATTGCTATCGCAATGGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTC +ATTGCTTCTTTCAGACTGTTTGCGCGTACGCGTTCCATGTGGTCATTCAATCCAGAAACTAACATTCTTC +TCAACGTGCCACTCCATGGCACTATTCTGACCAGACCGCTTCTAGAAAGTGAACTCGTAATCGGAGCTGT +GATCCTTCGTGGACATCTTCGTATTGCTGGACACCATCTAGGACGCTGTGACATCAAGGACCTGCCTAAA +GAAATCACTGTTGCTACATCACGAACGCTTTCTTATTACAAATTGGGAGCTTCGCAGCGTGTAGCAGGTG +ACTCAGGTTTTGCTGCATACAGTCGCTACAGGATTGGCAACTATAAATTAAACACAGACCATTCCAGTAG +CAGTGACAATATTGCTTTGCTTGTACAGTAAGTGACAACAGATGTTTCATCTCGTTGACTTTCAGGTTAC +TATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATA +AACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAAC +CAATGGAGATTGATTAAACGAACATGAAAATTATTCTTTTCTTGGCACTGATAACACTCGCTACTTGTGA +GCTTTATCACTACCAAGAGTGTGTTAGAGGTACAACAGTACTTTTAAAAGAACCTTGCTCTTCTGGAACA +TACGAGGGCAATTCACCATTTCATCCTCTAGCTGATAACAAATTTGCACTGACTTGCTTTAGCACTCAAT +TTGCTTTTGCTTGTCCTGACGGCGTAAAACACGTCTATCAGTTACGTGCCAGATCAGTTTCACCTAAACT +GTTCATCAGACAAGAGGAAGTTCAAGAACTTTACTCTCCAATTTTTCTTATTGTTGCGGCAATAGTGTTT +ATAACACTTTGCTTCACACTCAAAAGAAAGACAGAATGATTGAACTTTCATTAATTGACTTCTATTTGTG +CTTTTTAGCCTTTCTGCTATTCCTTGTTTTAATTATGCTTATTATCTTTTGGTTCTCACTTGAACTGCAA +GATCATAATGAAACTTGTCACGCCTAAACGAACATGAAATTTCTTGTTTTCTTAGGAATCATCACAACTG +TAGCTGCATTTCACCAAGAATGTAGTTTACAGTCATGTACTCAACATCAACCATATGTAGTTGATGACCC +GTGTCCTATTCACTTCTATTCTAAATGGTATATTAGAGTAGGAGCTAGAAAATCAGCACCTTTAATTGAA +TTGTGCGTGGATGAGGCTGGTTCTAAATCACCCATTCAGTACATCGATATCGGTAATTATACAGTTTCCT +GTTTACCTTTTACAATTAATTGCCAGGAACCTAAATTGGGTAGTCTTGTAGTGCGTTGTTCGTTCTATGA +AGACTTTTTAGAGTATCATGACGTTCGTGTTGTTTTAGATTTCATCTAAACGAACAAACTAAAATGTCTG +ATAATGGACCCCAAAATCAGCGAAATGCACCCCGCATTACGTTTGGTGGACCCTCAGATTCAACTGGCAG +TAACCAGAATGGAGAACGCAGTGGGGCGCGATCAAAACAACGTCGGCCCCAAGGTTTACCCAATAATACT +GCGTCTTGGTTCACCGCTCTCACTCAACATGGCAAGGAAGACCTTAAATTCCCTCGAGGACAAGGCGTTC +CAATTAACACCAATAGCAGTCCAGATGACCAAATTGGCTACTACCGAAGAGCTACCAGACGAATTCGTGG +TGGTGACGGTAAAATGAAAGATCTCAGTCCAAGATGGTATTTCTACTACCTAGGAACTGGGCCAGAAGCT +GGACTTCCCTATGGTGCTAACAAAGACGGCATCATATGGGTTGCAACTGAGGGAGCCTTGAATACACCAA +AAGATCACATTGGCACCCGCAATCCTGCTAACAATGCTGCAATCGTGCTACAACTTCCTCAAGGAACAAC +ATTGCCAAAAGGCTTCTACGCAGAAGGGAGCAGAGGCGGCAGTCAAGCCTCTTCTCGTTCCTCATCACGT +AGTCGCAACAGTTCAAGAAATTCAACTCCAGGCAGCAGTAGGGGAACTTCTCCTGCTAGAATGGCTGGCA +ATGGCGGTGATGCTGCTCTTGCTTTGCTGCTGCTTGACAGATTGAACCAGCTTGAGAGCAAAATGTCTGG +TAAAGGCCAACAACAACAAGGCCAAACTGTCACTAAGAAATCTGCTGCTGAGGCTTCTAAGAAGCCTCGG +CAAAAACGTACTGCCACTAAAGCATACAATGTAACACAAGCTTTCGGCAGACGTGGTCCAGAACAAACCC +AAGGAAATTTTGGGGACCAGGAACTAATCAGACAAGGAACTGATTACAAACATTGGCCGCAAATTGCACA +ATTTGCCCCCAGCGCTTCAGCGTTCTTCGGAATGTCGCGCATTGGCATGGAAGTCACACCTTCGGGAACG +TGGTTGACCTACACAGGTGCCATCAAATTGGATGACAAAGATCCAAATTTCAAAGATCAAGTCATTTTGC +TGAATAAGCATATTGACGCATACAAAACATTCCCACCAACAGAGCCTAAAAAGGACAAAAAGAAGAAGGC +TGATGAAACTCAAGCCTTACCGCAGAGACAGAAGAAACAGCAAACTGTGACTCTTCTTCCTGCTGCAGAT +TTGGATGATTTCTCCAAACAATTGCAACAATCCATGAGCAGTGCTGACTCAACTCAGGCCTAAACTCATG +CAGACCACACAAGGCAGATGGGCTATATAAACGTTTTCGCTTTTCCGTTTACGATATATAGTCTACTCTT +GTGCAGAATGAATTCTCGTAACTACATAGCACAAGTAGATGTAGTTAACTTTAATCTCACATAGCAATCT +TTAATCAGTGTGTAACATTAGGGAGGACTTGAAAGAGCCACCACATTTTCACCGAGGCCACGCGGAGTAC +GATCGAGTGTACAGTGAACAATGCTAGGGAGAGCTGCCTATATGGAAGAGCCCTAATGTGTAAAATTAAT +TTTAGTAGTGCTATCCCCATGTGATTTTAATAGCTTCTTAGGAGAATGACAAAAAAAAAAAAAAAAAAAA +AAAAAAAAAAAAA diff --git a/test/test_all.py b/test/test_all.py index 28d9912..7612144 100644 --- a/test/test_all.py +++ b/test/test_all.py @@ -1,13 +1,13 @@ -import os import subprocess + from pathlib import Path import pytest import primaschema.lib as lib + data_dir = Path("test/data") -schema_dir = Path(os.environ["PRIMER_SCHEMES_PATH"]).resolve() / "schema" def run(cmd, cwd=data_dir): # Helper for CLI testing @@ -22,138 +22,233 @@ def test_cli_version(): def test_hash_ref(): assert ( - lib.hash_ref("test/data/primer-schemes/eden/v1/reference.fasta") - == "primaschema:7d5621cd3b3e498d" + lib.hash_ref( + "test/data/primer-schemes/schemes/sars-cov-2/eden/2500/v1.0.0/reference.fasta" + ) + == "primaschema:b1acd7163146bf17" ) def test_cli_hash_ref(): - run_cmd = run("primaschema hash-ref primer-schemes/eden/v1/reference.fasta") - assert "primaschema:7d5621cd3b3e498d" in run_cmd.stdout + run_cmd = run( + "primaschema hash-ref primer-schemes/schemes/sars-cov-2/eden/2500/v1.0.0/reference.fasta" + ) + assert "primaschema:b1acd7163146bf17" in run_cmd.stdout def test_cli_hash_primer_bed(): - run_cmd = run("primaschema hash-bed primer-schemes/artic/v4.1/primer.bed") - assert "primaschema:9005b441227985c8" in run_cmd.stdout + run_cmd = run( + "primaschema hash-bed primer-schemes/schemes/sars-cov-2/artic/400/v4.1.0/primer.bed" + ) + assert "primaschema:3ef3e7bb23008684" in run_cmd.stdout def test_cli_scheme_bed(): - run_cmd = run("primaschema hash-bed primer-schemes/artic/v4.1/scheme.bed") - assert "primaschema:9005b441227985c8" in run_cmd.stdout + run_cmd = run( + "primaschema hash-bed primer-schemes/schemes/sars-cov-2/artic/400/v4.1.0/scheme.bed" + ) + assert "primaschema:3ef3e7bb23008684" in run_cmd.stdout def test_artic_v41_scheme_hash_matches_primer_hash(): scheme_bed_hash = lib.hash_scheme_bed( - "test/data/primer-schemes/artic/v4.1/scheme.bed", - "test/data/primer-schemes/artic/v4.1/reference.fasta", + "test/data/primer-schemes/schemes/sars-cov-2/artic/400/v4.1.0/scheme.bed", + "test/data/primer-schemes/schemes/sars-cov-2/artic/400/v4.1.0/reference.fasta", ) primer_bed_hash = lib.hash_primer_bed( - "test/data/primer-schemes/artic/v4.1/primer.bed" + "test/data/primer-schemes/schemes/sars-cov-2/artic/400/v4.1.0/primer.bed" ) assert scheme_bed_hash == primer_bed_hash -def test_eden_v1_schema(): - lib.validate_with_linkml_schema( - data_dir / "primer-schemes/eden/v1/info.yml", - schema_dir / "primer_scheme.yml", +def test_valid_eden_v1(): + lib.validate( + data_dir / "primer-schemes/schemes/sars-cov-2/eden/2500/v1.0.0", + ) + lib.validate( + data_dir / "primer-schemes/schemes/sars-cov-2/eden/2500/v1.0.0", + full=True, ) -def test_artic_v41_schema(): - lib.validate_with_linkml_schema( - data_dir / "primer-schemes/artic/v4.1/info.yml", - schema_dir / "primer_scheme.yml", +def test_valid_artic_v41(): + lib.validate( + data_dir / "primer-schemes/schemes/sars-cov-2/artic/400/v4.1.0", ) -# Needs updating since reverting hash function to consume coordinates again. Needs BEDs creating for this case -# def test_checksum_case_normalisation(): -# seqs_a = ["ACGT", "CAGT"] -# seqs_b = ["ACGT", "cagt"] -# assert lib.hash_sequences(seqs_a) == lib.hash_sequences(seqs_b) def test_checksum_case_normalisation(): assert lib.hash_bed( - data_dir / "broken/different-case/eden-v1.primer.bed" - ) == lib.hash_bed(data_dir / "broken/different-case/eden-v1-modified.primer.bed") - + data_dir / "primer-schemes/schemes/sars-cov-2/eden/2500/v1.0.0/primer.bed" + ) == lib.hash_bed(data_dir / "different-case/eden.modified.primer.bed") -def test_validate_artic_v41(): - lib.validate(data_dir / "primer-schemes/artic/v4.1") +def test_cli_valid_recursive(): + run("primaschema validate --recursive primer-schemes") -def test_validate_fail_five_columns(): - with pytest.raises(RuntimeError): - lib.validate(data_dir / "broken/five-columns") - -def test_validate_recursive(): - run_cmd = "primaschema validate-recursive primer-schemes" +def test_valid_rebuild(): + lib.validate( + data_dir / "primer-schemes/schemes/sars-cov-2/eden/2500/v1.0.0", + rebuild=True, + ) def test_hash_bed(): - lib.hash_bed(data_dir / "primer-schemes/artic/v4.1/primer.bed") - lib.hash_bed(data_dir / "primer-schemes/artic/v4.1/scheme.bed") - - -def test_build_from_primer_bed(): - run_cmd = run("primaschema build primer-schemes/artic/v4.1 --force") - run("rm -rf artic-v4.1") + lib.hash_bed( + data_dir / "primer-schemes/schemes/sars-cov-2/artic/400/v4.1.0/primer.bed" + ) + lib.hash_bed( + data_dir / "primer-schemes/schemes/sars-cov-2/artic/400/v4.1.0/scheme.bed" + ) -def test_build_from_scheme_bed(): - run_cmd = run("primaschema build primer-schemes/eden/v1 --force") - run("rm -rf eden-v1") +def test_build(): + run("primaschema build primer-schemes/schemes/sars-cov-2/artic/400/v4.1.0") + run("rm -rf artic-v4.1.0") def test_build_recursive(): - lib.build_recursive(data_dir / "primer-schemes", force=True) - run("rm -rf built", cwd="./") + lib.build(data_dir / "primer-schemes", recursive=True) + run("rm -rf built") def test_build_manifest(): - lib.build_manifest(root_dir=data_dir / "primer-schemes", schema_dir=schema_dir) + lib.build_manifest(root_dir=data_dir / "primer-schemes") + run("rm -rf built index.json", cwd="./") def test_primer_bed_to_scheme_bed(): - lib.convert_primer_bed_to_scheme_bed( - bed_path=data_dir / "primer-schemes/artic/v4.1/primer.bed" + scheme_bed_path = ( + data_dir / "primer-schemes/schemes/sars-cov-2/artic/400/v4.1.0/scheme.bed" + ) + primer_bed_path = ( + data_dir / "primer-schemes/schemes/sars-cov-2/artic/400/v4.1.0/primer.bed" ) - lib.parse_scheme_bed("scheme.bed") - run("rm -rf scheme.bed", cwd="./") + bed_str = lib.convert_primer_bed_to_scheme_bed(bed_path=primer_bed_path) + with open(scheme_bed_path) as fh: + expected_bed_str = fh.read() + assert bed_str == expected_bed_str def test_scheme_bed_to_primer_bed(): - lib.convert_scheme_bed_to_primer_bed( - bed_path=data_dir / "primer-schemes/artic/v4.1/scheme.bed", - fasta_path=data_dir / "primer-schemes/artic/v4.1/reference.fasta", + scheme_bed_path = ( + data_dir / "primer-schemes/schemes/sars-cov-2/artic/400/v4.1.0/scheme.bed" + ) + primer_bed_path = ( + data_dir / "primer-schemes/schemes/sars-cov-2/artic/400/v4.1.0/primer.bed" ) - lib.parse_primer_bed("primer.bed") - run("rm -rf primer.bed", cwd="./") + reference_path = ( + data_dir / "primer-schemes/schemes/sars-cov-2/artic/400/v4.1.0/reference.fasta" + ) + bed_str = lib.convert_scheme_bed_to_primer_bed( + bed_path=scheme_bed_path, fasta_path=reference_path + ) + with open(primer_bed_path) as fh: + expected_bed_str = fh.read() + assert bed_str == expected_bed_str def test_diff(): run_cmd = run( - "primaschema diff primer-schemes/midnight/v1/primer.bed primer-schemes/midnight/v2/primer.bed" + "primaschema diff primer-schemes/schemes/sars-cov-2/midnight/1200/v1.0.0/primer.bed primer-schemes/schemes/sars-cov-2/midnight/1200/v2.0.0/primer.bed" ) assert ( - """chrom chromStart chromEnd name poolName strand sequence origin -MN908947.3 27784 27808 SARS-CoV-2_28_LEFT_27837T 2 + TTTGTGCTTTTTAGCCTTTCTGTT bed2""" - == run_cmd.stdout.strip() + """SARS-CoV-2_28_LEFT_2""" in run_cmd.stdout.strip() + and len(run_cmd.stdout.strip().split("\n")) == 2 ) def test_calculate_intervals(): - all_intervals = lib.compute_intervals(data_dir / "primer-schemes/artic/v4.1/primer.bed") - assert 'MN908947.3' in all_intervals - intervals = all_intervals['MN908947.3'] - assert 'SARS-CoV-2_99' in intervals - assert intervals['SARS-CoV-2_99'] == (29452, 29854) + all_intervals = lib.amplicon_intervals( + data_dir / "primer-schemes/schemes/sars-cov-2/artic/400/v4.1.0/primer.bed" + ) + assert "MN908947.3" in all_intervals + intervals = all_intervals["MN908947.3"] + assert "SARS-CoV-2_99" in intervals + assert intervals["SARS-CoV-2_99"] == (29452, 29854) def test_print_intervals(): - run_cmd = run("primaschema intervals primer-schemes/artic/v4.1/primer.bed") + run_cmd = run( + "primaschema show-intervals primer-schemes/schemes/sars-cov-2/artic/400/v4.1.0/primer.bed" + ) + assert """MN908947.3\t29452\t29854\tSARS-CoV-2_99\n""" in run_cmd.stdout - assert ( - """MN908947.3\t29452\t29854\tSARS-CoV-2_99\n""" in run_cmd.stdout - ) \ No newline at end of file + +def test_plot_single_ref_chrom_ref(): + lib.plot_primers( + data_dir / "primer-schemes/schemes/sars-cov-2/artic/400/v4.1.0/primer.bed", + ) + run("rm -rf primer.html", cwd="./") + + +def test_plot_many_ref_chroms_ref(): + lib.plot_primers(data_dir / "many-ref-chroms/primer.bed") + run("rm -rf primer.html", cwd="./") + + +def test_6to7_many_ref_chroms(): + scheme_bed_path = data_dir / "many-ref-chroms/scheme.bed" + primer_bed_path = data_dir / "many-ref-chroms/primer.bed" + reference_path = data_dir / "many-ref-chroms/reference.fasta" + bed_str = lib.convert_scheme_bed_to_primer_bed( + bed_path=scheme_bed_path, fasta_path=reference_path + ) + with open(primer_bed_path) as fh: + expected_bed_str = fh.read() + assert bed_str == expected_bed_str + + +def test_invalid_duplicate_primers(): + with pytest.raises(ValueError): # Also catches pydantic.ValidationError + lib.validate( + data_dir / "broken/duplicated-primers", + ) + + +def test_invalid_primer_bounds(): + with pytest.raises(ValueError): # Also catches pydantic.ValidationError + lib.validate( + data_dir / "broken/primer-bounds", + ) + + +def test_invalid_amplicon_tiling(): + with pytest.raises(ValueError): # Also catches pydantic.ValidationError + lib.validate( + data_dir / "broken/non-tiling", + ) + + +def test_format_primer_bed(): + """Sort BED into maximally compatible output order""" + assert lib.format_primer_bed(data_dir / "unordered/primer.bed").strip() == ( + """MN908947.3 25 50 SARS-CoV-2_1_LEFT_1 1 + AACAAACCAACCAACTTTCGATCTC +MN908947.3 408 431 SARS-CoV-2_1_RIGHT_1 1 - CTTCTACTAAGCCACAAGTGCCA +MN908947.3 324 344 SARS-CoV-2_2_LEFT_1 2 + TTTACAGGTTCGCGACGTGC +MN908947.3 705 727 SARS-CoV-2_2_RIGHT_1 2 - ATAAGGATCAGTGCCAAGCTCG""" + ) + + +def test_invalid_missing_field(): + with pytest.raises(ValueError): # Also catches pydantic.ValidationError + lib.validate(data_dir / "broken/info-yml/missing-field") + lib.validate(data_dir / "broken/info-yml/missing-field", full=True) + + +def test_invalid_extra_field(): + with pytest.raises(ValueError): # Also catches pydantic.ValidationError + lib.validate(data_dir / "broken/info-yml/extra-field") + lib.validate(data_dir / "broken/info-yml/extra-field", full=True) + + +def test_subset(): + lib.subset(scheme_dir=data_dir / "many-ref-chroms", chrom="NC_038235.1") + df = lib.parse_primer_bed("built/primer.bed") + assert len(df) == 4 + run("rm -rf built", cwd="./") + + +def test_commented_bed(): + lib.validate(data_dir / "bed-comment")