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Mapq fitlering #221

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Mapq fitlering #221

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4386392
actions: Attempt to fix env file path.
wwood May 23, 2024
aeadc5c
actions
wwood May 23, 2024
b2829fb
actions
wwood May 23, 2024
4b2093c
actions
wwood May 23, 2024
c1e225f
filter: Towards MAPQ filtering.
wwood Sep 16, 2024
9cf7a00
mapq filtering: Implement it.
wwood Sep 17, 2024
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56 changes: 28 additions & 28 deletions .github/workflows/test-coverm.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -9,13 +9,13 @@ jobs:
fail-fast: false
matrix:
os: ["ubuntu-latest"]
python-version: ["3.11"]
# python-version: ["3.11"]
steps:
- uses: conda-incubator/setup-miniconda@v3
with:
auto-update-conda: true
python-version: ${{ matrix.python-version }}
environment-file: coverm.yml
# auto-update-conda: true
# python-version: ${{ matrix.python-version }}
environment-file: environment.yml
channels: conda-forge,defaults,bioconda
- name: Conda info
shell: bash -el {0}
Expand All @@ -26,27 +26,27 @@ jobs:
- name: Run test
run: |
cargo test
miniconda_osx:
name: miniconda_osx (${{ matrix.python-version }}, ${{ matrix.os }})
runs-on: ${{ matrix.os }}
strategy:
fail-fast: false
matrix:
os: ["macos-latest"]
python-version: ["3.11"]
steps:
- uses: conda-incubator/setup-miniconda@v3
with:
auto-update-conda: true
python-version: ${{ matrix.python-version }}
environment-file: coverm-osx.yml
channels: conda-forge,defaults,bioconda
- name: Conda info
shell: bash -el {0}
run: conda info
- name: Conda list
shell: pwsh
run: conda list
- name: Run test
run: |
cargo test -- --skip bwa_mem2
# miniconda_osx:
# name: miniconda_osx (${{ matrix.python-version }}, ${{ matrix.os }})
# runs-on: ${{ matrix.os }}
# strategy:
# fail-fast: false
# matrix:
# os: ["macos-latest"]
# python-version: ["3.11"]
# steps:
# - uses: conda-incubator/setup-miniconda@v3
# with:
# auto-update-conda: true
# python-version: ${{ matrix.python-version }}
# environment-file: ../coverm-osx.yml
# channels: conda-forge,defaults,bioconda
# - name: Conda info
# shell: bash -el {0}
# run: conda info
# - name: Conda list
# shell: pwsh
# run: conda list
# - name: Run test
# run: |
# cargo test -- --skip bwa_mem2
1 change: 1 addition & 0 deletions Cargo.toml
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Expand Up @@ -12,6 +12,7 @@ exclude = [ # Max upload is 10MB, as of writing test data was 15MB
"tests/*",
]
default-run = "coverm"
edition = "2015"

[dependencies]
bio = "1.1.0"
Expand Down
0 coverm.yml → environment.yml
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6 changes: 6 additions & 0 deletions src/bam_generator.rs
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Expand Up @@ -486,6 +486,7 @@ pub fn generate_filtered_bam_readers_from_bam_files(
min_aligned_length_single: u32,
min_percent_identity_single: f32,
min_aligned_percent_single: f32,
min_mapq: u8,
min_aligned_length_pair: u32,
min_percent_identity_pair: f32,
min_aligned_percent_pair: f32,
Expand All @@ -511,6 +512,7 @@ pub fn generate_filtered_bam_readers_from_bam_files(
min_aligned_length_single,
min_percent_identity_single,
min_aligned_percent_single,
min_mapq,
min_aligned_length_pair,
min_percent_identity_pair,
min_aligned_percent_pair,
Expand Down Expand Up @@ -544,6 +546,7 @@ pub struct StreamingFilteredNamedBamReaderGenerator {
min_aligned_length_single: u32,
min_percent_identity_single: f32,
min_aligned_percent_single: f32,
min_mapq: u8,
min_aligned_length_pair: u32,
min_percent_identity_pair: f32,
min_aligned_percent_pair: f32,
Expand Down Expand Up @@ -584,6 +587,7 @@ impl NamedBamReaderGenerator<StreamingFilteredNamedBamReader>
self.min_aligned_length_single,
self.min_percent_identity_single,
self.min_aligned_percent_single,
self.min_mapq,
self.min_aligned_length_pair,
self.min_percent_identity_pair,
self.min_aligned_percent_pair,
Expand Down Expand Up @@ -651,6 +655,7 @@ pub fn generate_filtered_named_bam_readers_from_reads(
min_aligned_length_single: u32,
min_percent_identity_single: f32,
min_aligned_percent_single: f32,
min_mapq: u8,
min_aligned_length_pair: u32,
min_percent_identity_pair: f32,
min_aligned_percent_pair: f32,
Expand Down Expand Up @@ -682,6 +687,7 @@ pub fn generate_filtered_named_bam_readers_from_reads(
min_aligned_length_single,
min_percent_identity_single,
min_aligned_percent_single,
min_mapq,
min_aligned_length_pair,
min_percent_identity_pair,
min_aligned_percent_pair,
Expand Down
7 changes: 7 additions & 0 deletions src/bin/coverm.rs
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Expand Up @@ -165,6 +165,7 @@ fn main() {
filter_params.min_aligned_length_single,
filter_params.min_percent_identity_single,
filter_params.min_aligned_percent_single,
filter_params.min_mapq,
filter_params.min_aligned_length_pair,
filter_params.min_percent_identity_pair,
filter_params.min_aligned_percent_pair,
Expand Down Expand Up @@ -463,6 +464,7 @@ fn main() {
filter_params.min_aligned_length_single,
filter_params.min_percent_identity_single,
filter_params.min_aligned_percent_single,
filter_params.min_mapq,
filter_params.min_aligned_length_pair,
filter_params.min_percent_identity_pair,
filter_params.min_aligned_percent_pair,
Expand Down Expand Up @@ -519,6 +521,7 @@ fn main() {
filter_params.min_aligned_length_single,
filter_params.min_percent_identity_single,
filter_params.min_aligned_percent_single,
filter_params.min_mapq,
filter_params.min_aligned_length_pair,
filter_params.min_percent_identity_pair,
filter_params.min_aligned_percent_pair,
Expand Down Expand Up @@ -1209,6 +1212,7 @@ struct FilterParameters {
min_aligned_length_single: u32,
min_percent_identity_single: f32,
min_aligned_percent_single: f32,
min_mapq: u8, // 255 indicates no filtering
min_aligned_length_pair: u32,
min_percent_identity_pair: f32,
min_aligned_percent_pair: f32,
Expand All @@ -1224,6 +1228,7 @@ impl FilterParameters {
min_aligned_length_single: *m.get_one::<u32>("min-read-aligned-length").unwrap_or(&0),
min_percent_identity_single: parse_percentage(m, "min-read-percent-identity"),
min_aligned_percent_single: parse_percentage(m, "min-read-aligned-percent"),
min_mapq: *m.get_one::<u8>("min-mapq").unwrap_or(&255),
min_aligned_length_pair: *m
.get_one::<u32>("min-read-aligned-length-pair")
.unwrap_or(&0),
Expand Down Expand Up @@ -1253,6 +1258,7 @@ impl FilterParameters {
self.min_percent_identity_single > 0.0
|| self.min_percent_identity_pair > 0.0
|| self.min_aligned_percent_single > 0.0
|| self.min_mapq < 255
|| self.min_aligned_percent_pair > 0.0
|| self.min_aligned_length_single > 0
|| self.min_aligned_length_pair > 0
Expand Down Expand Up @@ -1578,6 +1584,7 @@ fn get_streamed_filtered_bam_readers(
filter_params.min_aligned_length_single,
filter_params.min_percent_identity_single,
filter_params.min_aligned_percent_single,
filter_params.min_mapq,
filter_params.min_aligned_length_pair,
filter_params.min_percent_identity_pair,
filter_params.min_aligned_percent_pair,
Expand Down
25 changes: 25 additions & 0 deletions src/cli.rs
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Expand Up @@ -175,6 +175,16 @@ fn add_thresholding_options(manual: Manual) -> Manual {
default_roff("0")
)),
)
.option(Opt::new("INT").long("--min-mapq").help(&format!(
"Exclude reads with a mapping quality \
below this value. An INT between 0 and 254. \
When thresholding pairs, both reads \
are excluded if either has a MAPQ below this value. \
If 0, \
reads with MAPQ of 255 (mapping quality unavailable) \
are excluded. {}",
default_roff("not set")
)))
.flag(
Flag::new()
.long("--proper-pairs-only")
Expand Down Expand Up @@ -1322,6 +1332,11 @@ Ben J. Woodcroft <benjwoodcroft near gmail.com>
.long("min-read-aligned-percent")
.value_parser(clap::value_parser!(f32)),
)
.arg(
Arg::new("min-mapq")
.long("min-mapq")
.value_parser(clap::value_parser!(u8)),
)
.arg(
Arg::new("min-read-aligned-length-pair")
.long("min-read-aligned-length-pair")
Expand Down Expand Up @@ -1707,6 +1722,11 @@ Ben J. Woodcroft <benjwoodcroft near gmail.com>
.long("min-read-aligned-percent")
.value_parser(clap::value_parser!(f32)),
)
.arg(
Arg::new("min-mapq")
.long("min-mapq")
.value_parser(clap::value_parser!(u8)),
)
.arg(
Arg::new("min-read-aligned-length-pair")
.long("min-read-aligned-length-pair")
Expand Down Expand Up @@ -1845,6 +1865,11 @@ Ben J. Woodcroft <benjwoodcroft near gmail.com>
.long("min-read-percent-identity")
.value_parser(clap::value_parser!(f32)),
)
.arg(
Arg::new("min-mapq")
.long("min-mapq")
.value_parser(clap::value_parser!(u8)),
)
.arg(
Arg::new("min-read-aligned-percent")
.long("min-read-aligned-percent")
Expand Down
1 change: 0 additions & 1 deletion src/contig.rs
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Expand Up @@ -273,7 +273,6 @@ mod tests {
use mapping_index_maintenance::VanillaIndexStruct;
use mapping_parameters::*;
use shard_bam_reader::*;
use std::io::Read;
use std::str;
use OutputWriter;

Expand Down
1 change: 0 additions & 1 deletion src/coverage_printer.rs
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Expand Up @@ -544,7 +544,6 @@ pub fn print_dense_cached_coverage_taker(
mod tests {
use super::*;
use std::io::Cursor;
use std::io::Read;
use std::str;
use OutputWriter;

Expand Down
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