From 76cfd15694915c08f834020390fc2c319249e5d8 Mon Sep 17 00:00:00 2001
From: LaraFuhrmann <55209716+LaraFuhrmann@users.noreply.github.com>
Date: Wed, 6 Sep 2023 17:05:37 +0200
Subject: [PATCH 01/25] working multiprocessing

---
 shorah/b2w.py     | 374 ++++++++++++++++++++++++++++------------------
 shorah/shotgun.py |   3 +-
 2 files changed, 231 insertions(+), 146 deletions(-)

diff --git a/shorah/b2w.py b/shorah/b2w.py
index ce7d571..92076ea 100644
--- a/shorah/b2w.py
+++ b/shorah/b2w.py
@@ -4,6 +4,8 @@
 import numpy as np
 import math
 import logging
+from multiprocessing import Process, Pool, cpu_count
+import os
 
 def _write_to_file(lines, file_name):
     with open(file_name, "w") as f:
@@ -154,7 +156,6 @@ def _run_one_window(samfile, window_start, reference_name, window_length,
         base_pair_distr_in_window = np.zeros((window_length, len(alphabet)), dtype=int)
 
     for read in iter:
-
         if (read.reference_start is None) or (read.reference_end is None):
             continue
         first_aligned_pos = read.reference_start # this is 0-based
@@ -279,12 +280,189 @@ def _run_one_window(samfile, window_start, reference_name, window_length,
     return convert_to_printed_fmt(arr), arr_read_qualities_summary, arr_read_summary, counter, window_length, pos_filter
 
 
+def parallel_run_one_window(
+    reference_filename,
+    minimum_reads,
+    tiling,
+    region_end,
+    idx,
+    window_start,
+    window_length,
+    alignment_file,
+    reference_name,
+    win_min_ext,
+    permitted_reads_per_location,
+    counter,
+    exact_conformance_fix_0_1_basing_in_reads,
+    indel_map,
+    max_ins_at_pos,
+    extended_window_mode,
+    exclude_non_var_pos_threshold
+):
+    """
+    build one window.
+    """
+    reffile = pysam.FastaFile(reference_filename)
+
+    samfile = pysam.AlignmentFile(
+        alignment_file,
+        "r", # auto-detect bam/cram (rc)
+        reference_filename=reference_filename,
+        threads=1
+    )
+
+    reads = open(f"reads_{idx}.fas", "w")
+
+    logging.info(f"Working on window (1-based) @ {window_start+1}")
+
+    (arr, arr_read_qualities_summary, arr_read_summary,
+     counter, control_window_length, pos_filter) = _run_one_window(
+        samfile,
+        window_start - 1, # make 0 based
+        reference_name,
+        window_length,
+        math.floor(win_min_ext * window_length),
+        dict(permitted_reads_per_location), # copys dict ("pass by value")
+        counter,
+        exact_conformance_fix_0_1_basing_in_reads,
+        indel_map,
+        max_ins_at_pos,
+        extended_window_mode,
+        exclude_non_var_pos_threshold
+    )
+
+    logging.debug(f"Window length: {control_window_length}")
+
+    window_end = window_start + window_length - 1
+    file_name = f'w-{reference_name}-{window_start}-{window_end}'
+
+    # TODO solution for backward conformance
+    if len(tiling) > 1:
+        end_extended_by_a_window = region_end + (tiling[1][0]-tiling[0][0])*3
+    else:
+        end_extended_by_a_window = region_end + window_length*3
+
+    for read in arr_read_summary:
+        if idx == len(tiling) - 1 and read[1] > end_extended_by_a_window:
+            continue
+        # TODO reads.fas not FASTA conform, +-0/1 mixed
+        # TODO global end does not really make sense, only for conformance
+        # read name, global start, global end, read start, read end, read
+        reads.write(
+            f'{read[0]}\t{tiling[0][0]-1}\t{end_extended_by_a_window}\t{read[1]}\t{read[2]}\t{read[3]}\n'
+        )
+
+    reads.close()
+
+    if (idx != len(tiling) - 1 # except last
+        and len(arr) > 0) or len(tiling) == 1: # suppress output if window empty
+
+        _write_to_file(arr, file_name + '.reads.fas')
+        if arr_read_qualities_summary is not None:
+            with open(file_name + '.qualities.npy', 'wb') as f:
+                np.save(f, np.asarray(arr_read_qualities_summary, dtype=np.int64), allow_pickle=True)
+
+        ref = reffile.fetch(reference=reference_name, start=window_start-1, end=window_end)
+
+        if extended_window_mode:
+            for file_name_comp, char in [("extended-ref", "X"), ("ref", "-")]:
+                res_ref = _build_one_full_read(
+                    list(ref), list(ref), None, None,
+                    window_start-1, window_end-1,
+                    indel_map, max_ins_at_pos, extended_window_mode, char
+                )[0]
+
+                k = max(0, control_window_length - len(res_ref))
+                res_ref += k * "N"
+                assert_condition = control_window_length == len(res_ref)
+
+                if exclude_non_var_pos_threshold > 0 and file_name_comp == "ref":
+                    _write_to_file([
+                        f'>{reference_name} {window_start}\n' + res_ref
+                    ], file_name + '.envp-full-ref.fas')
+
+                    envp_ref = np.array(list(res_ref))
+                    envp_ref[~pos_filter] = "="
+                    _write_to_file([
+                        f'>{reference_name} {window_start}\n' + "".join(envp_ref)
+                    ], file_name + '.envp-ref.fas')
+
+                    reduced_ref = np.array(list(res_ref))[pos_filter]
+                    res_ref = "".join(reduced_ref)
+                    assert_condition = (control_window_length ==
+                                        len(reduced_ref) + len(pos_filter) - pos_filter.sum())
+
+                _write_to_file([
+                    f'>{reference_name} {window_start}\n' + res_ref
+                ], f'{file_name}.{file_name_comp}.fas')
+
+                assert assert_condition, (
+                    f"""
+                        Reference ({file_name_comp}) does not have same length as the window.
+                        Location: {file_name}
+                        Ref: {len(res_ref)}
+                        Win: {control_window_length}
+                    """
+                )
+
+        else:
+            k = max(0, control_window_length - len(ref))
+            ref += k * "N"
+
+            if exclude_non_var_pos_threshold > 0:
+                full_file_name = file_name + '.envp-full-ref.fas'
+            else:
+                full_file_name = file_name + '.ref.fas'
+
+            _write_to_file([
+                f'>{reference_name} {window_start}\n' + ref
+            ], full_file_name)
+
+            assert control_window_length == len(ref), (
+                f"""
+                    Reference does not have same length as the window.
+                    Location: {file_name}
+                    Ref: {len(ref)}
+                    Win: {control_window_length}
+                """
+            )
+
+            if exclude_non_var_pos_threshold > 0:
+                envp_ref = np.array(list(ref))
+                envp_ref[~pos_filter] = "="
+                _write_to_file([
+                    f'>{reference_name} {window_start}\n' + "".join(envp_ref)
+                ], file_name + '.envp-ref.fas')
+                reduced_ref = np.array(list(ref))[pos_filter]
+                _write_to_file([
+                    f'>{reference_name} {window_start}\n' + "".join(reduced_ref)
+                ], file_name + '.ref.fas')
+
+                assert (control_window_length == len(envp_ref) and
+                        control_window_length == len(reduced_ref) + len(pos_filter) - pos_filter.sum()), (
+                    f"""
+                        Reference does not have same length as the window.
+                        Location: {file_name}
+                        Envp Ref: {len(envp_ref)}
+                        Ref: {len(reduced_ref)}
+                        Win: {control_window_length}
+                    """
+                )
+
+        if len(arr) > minimum_reads:
+            line = (
+                f'{file_name}.reads.fas\t{reference_name}\t{window_start}\t'
+                f'{window_end}\t{len(arr)}'
+            )
+            _write_to_file([line], f"coverage_{idx}.txt")
+
 def build_windows(alignment_file: str, tiling_strategy: TilingStrategy,
     win_min_ext: float, maximum_reads: int, minimum_reads: int,
     reference_filename: str,
     exact_conformance_fix_0_1_basing_in_reads: Optional[bool] = False,
     extended_window_mode: Optional[bool] = False,
-    exclude_non_var_pos_threshold: Optional[float] = -1) -> None:
+    exclude_non_var_pos_threshold: Optional[float] = -1,
+    maxthreads: Optional[int] = 1) -> None:
     """Summarizes reads aligned to reference into windows.
     Three products are created:
     #. Multiple FASTA files (one for each window position)
@@ -314,6 +492,10 @@ def build_windows(alignment_file: str, tiling_strategy: TilingStrategy,
             positions are excluded. Set to -1 if no position should be excluded
             (the default).
     """
+    max_proc = min(max(cpu_count() - 1, 1), maxthreads)
+    logging.info('CPU(s) count %u,  will run %u build_windows', cpu_count(), max_proc)
+
+
     assert 0 <= win_min_ext <= 1
     assert (0 <= exclude_non_var_pos_threshold <= 1 or
             exclude_non_var_pos_threshold == -1)
@@ -323,12 +505,9 @@ def build_windows(alignment_file: str, tiling_strategy: TilingStrategy,
         alignment_file,
         "r", # auto-detect bam/cram (rc)
         reference_filename=reference_filename,
-        threads=1
+        threads=max_proc #1
     )
-    reffile = pysam.FastaFile(reference_filename)
-
-    cov_arr = []
-    reads = open("reads.fas", "w")
+    #reffile = pysam.FastaFile(reference_filename) --> we need to read it in each child process
     counter = 0
     reference_name = tiling_strategy.get_reference_name()
     tiling = tiling_strategy.get_window_tilings()
@@ -340,151 +519,56 @@ def build_windows(alignment_file: str, tiling_strategy: TilingStrategy,
         maximum_reads
     )
 
+    all_processes = []
     for idx, (window_start, window_length) in enumerate(tiling):
-        logging.info(f"Working on window (1-based) @ {window_start+1}")
-        (arr, arr_read_qualities_summary, arr_read_summary,
-         counter, control_window_length, pos_filter) = _run_one_window(
-            samfile,
-            window_start - 1, # make 0 based
-            reference_name,
-            window_length,
-            math.floor(win_min_ext * window_length),
-            dict(permitted_reads_per_location), # copys dict ("pass by value")
-            counter,
-            exact_conformance_fix_0_1_basing_in_reads,
-            indel_map,
-            max_ins_at_pos,
-            extended_window_mode,
-            exclude_non_var_pos_threshold
-        )
-        logging.debug(f"Window length: {control_window_length}")
-
-        window_end = window_start + window_length - 1
-        file_name = f'w-{reference_name}-{window_start}-{window_end}'
-
-        # TODO solution for backward conformance
-        if len(tiling) > 1:
-            end_extended_by_a_window = region_end + (tiling[1][0]-tiling[0][0])*3
-        else:
-            end_extended_by_a_window = region_end + window_length*3
-
-        for read in arr_read_summary:
-            if idx == len(tiling) - 1 and read[1] > end_extended_by_a_window:
-                continue
-            # TODO reads.fas not FASTA conform, +-0/1 mixed
-            # TODO global end does not really make sense, only for conformance
-            # read name, global start, global end, read start, read end, read
-            reads.write(
-                f'{read[0]}\t{tiling[0][0]-1}\t{end_extended_by_a_window}\t{read[1]}\t{read[2]}\t{read[3]}\n'
-            )
-
-        if (idx != len(tiling) - 1 # except last
-            and len(arr) > 0) or len(tiling) == 1: # suppress output if window empty
-
-            _write_to_file(arr, file_name + '.reads.fas')
-            if arr_read_qualities_summary is not None:
-                with open(file_name + '.qualities.npy', 'wb') as f:
-                    np.save(f, np.asarray(arr_read_qualities_summary, dtype=np.int64), allow_pickle=True)
-
-            ref = reffile.fetch(reference=reference_name, start=window_start-1, end=window_end)
-
-            if extended_window_mode:
-                for file_name_comp, char in [("extended-ref", "X"), ("ref", "-")]:
-                    res_ref = _build_one_full_read(
-                        list(ref), list(ref), None, None,
-                        window_start-1, window_end-1,
-                        indel_map, max_ins_at_pos, extended_window_mode, char
-                    )[0]
-
-                    k = max(0, control_window_length - len(res_ref))
-                    res_ref += k * "N"
-                    assert_condition = control_window_length == len(res_ref)
-
-                    if exclude_non_var_pos_threshold > 0 and file_name_comp == "ref":
-                        _write_to_file([
-                            f'>{reference_name} {window_start}\n' + res_ref
-                        ], file_name + '.envp-full-ref.fas')
-
-                        envp_ref = np.array(list(res_ref))
-                        envp_ref[~pos_filter] = "="
-                        _write_to_file([
-                            f'>{reference_name} {window_start}\n' + "".join(envp_ref)
-                        ], file_name + '.envp-ref.fas')
-
-                        reduced_ref = np.array(list(res_ref))[pos_filter]
-                        res_ref = "".join(reduced_ref)
-                        assert_condition = (control_window_length ==
-                                            len(reduced_ref) + len(pos_filter) - pos_filter.sum())
-
-                    _write_to_file([
-                        f'>{reference_name} {window_start}\n' + res_ref
-                    ], f'{file_name}.{file_name_comp}.fas')
-
-                    assert assert_condition, (
-                        f"""
-                            Reference ({file_name_comp}) does not have same length as the window.
-                            Location: {file_name}
-                            Ref: {len(res_ref)}
-                            Win: {control_window_length}
-                        """
-                    )
-
-            else:
-                k = max(0, control_window_length - len(ref))
-                ref += k * "N"
-
-                if exclude_non_var_pos_threshold > 0:
-                    full_file_name = file_name + '.envp-full-ref.fas'
-                else:
-                    full_file_name = file_name + '.ref.fas'
-
-                _write_to_file([
-                    f'>{reference_name} {window_start}\n' + ref
-                ], full_file_name)
-
-                assert control_window_length == len(ref), (
-                    f"""
-                        Reference does not have same length as the window.
-                        Location: {file_name}
-                        Ref: {len(ref)}
-                        Win: {control_window_length}
-                    """
+        p = Process(
+            target=parallel_run_one_window,
+            args=(
+                reference_filename,
+                minimum_reads,
+                tiling,
+                region_end,
+                idx,
+                window_start,
+                window_length,
+                alignment_file,
+                reference_name,
+                win_min_ext,
+                permitted_reads_per_location,
+                counter,
+                exact_conformance_fix_0_1_basing_in_reads,
+                indel_map,
+                max_ins_at_pos,
+                extended_window_mode,
+                exclude_non_var_pos_threshold,
                 )
+            )
+        p.start()
+        all_processes.append(p)
 
-                if exclude_non_var_pos_threshold > 0:
-                    envp_ref = np.array(list(ref))
-                    envp_ref[~pos_filter] = "="
-                    _write_to_file([
-                        f'>{reference_name} {window_start}\n' + "".join(envp_ref)
-                    ], file_name + '.envp-ref.fas')
-                    reduced_ref = np.array(list(ref))[pos_filter]
-                    _write_to_file([
-                        f'>{reference_name} {window_start}\n' + "".join(reduced_ref)
-                    ], file_name + '.ref.fas')
-
-                    assert (control_window_length == len(envp_ref) and
-                            control_window_length == len(reduced_ref) + len(pos_filter) - pos_filter.sum()), (
-                        f"""
-                            Reference does not have same length as the window.
-                            Location: {file_name}
-                            Envp Ref: {len(envp_ref)}
-                            Ref: {len(reduced_ref)}
-                            Win: {control_window_length}
-                        """
-                    )
-
-            if len(arr) > minimum_reads:
-                line = (
-                    f'{file_name}.reads.fas\t{reference_name}\t{window_start}\t'
-                    f'{window_end}\t{len(arr)}'
-                )
-                cov_arr.append(line)
+    for p in all_processes:
+      p.join()
+    print("here after join")
 
     samfile.close()
-    reads.close()
 
-    _write_to_file(cov_arr, "coverage.txt")
+    with open('reads.fas', 'w') as output_file:
+        for file_path in [f"reads_{idx}.fas" for idx in range(len(tiling))]:
+            with open(file_path, 'r') as input_file:
+                for line in input_file:
+                    output_file.write(line)
+            os.remove(file_path)
 
+    cov_arr = []
+    with open("coverage.txt", 'w') as output_file:
+        for file_path in [f"coverage_{idx}.txt" for idx in range(len(tiling))]:
+            try:
+                with open(file_path, 'r') as input_file:
+                    for line in input_file:
+                        output_file.write(line)
+                os.remove(file_path)
+            except Exception:
+                pass
 
 if __name__ == "__main__":
     import argparse
diff --git a/shorah/shotgun.py b/shorah/shotgun.py
index 127d85b..81d5698 100644
--- a/shorah/shotgun.py
+++ b/shorah/shotgun.py
@@ -469,7 +469,8 @@ def main(args):
             cov_thrd,
             in_fasta,
             extended_window_mode=extended_window_mode,
-            exclude_non_var_pos_threshold=exclude_non_var_pos_threshold
+            exclude_non_var_pos_threshold=exclude_non_var_pos_threshold,
+            maxthreads=maxthreads
         )
         logging.info('finished b2w')
 

From b2f8e52bc1ffaeebf0bceab904748f8a23022186 Mon Sep 17 00:00:00 2001
From: LaraFuhrmann <55209716+LaraFuhrmann@users.noreply.github.com>
Date: Fri, 8 Sep 2023 16:02:18 +0200
Subject: [PATCH 02/25] counter and control_window_length are now computed in
 advance of _run_one_window()

---
 shorah/b2w.py | 67 ++++++++++++++++++++++++++++++++++++++++++---------
 1 file changed, 56 insertions(+), 11 deletions(-)

diff --git a/shorah/b2w.py b/shorah/b2w.py
index 92076ea..8a71874 100644
--- a/shorah/b2w.py
+++ b/shorah/b2w.py
@@ -129,7 +129,7 @@ def _build_one_full_read(full_read: list[str], full_qualities: list[int]|list[st
     return full_read, full_qualities # TODO return same data type twice
 
 
-def _run_one_window(samfile, window_start, reference_name, window_length,
+def _run_one_window(samfile, window_start, reference_name, window_length,control_window_length,
         minimum_overlap, permitted_reads_per_location, counter,
         exact_conformance_fix_0_1_basing_in_reads, indel_map, max_ins_at_pos,
         extended_window_mode, exclude_non_var_pos_threshold):
@@ -144,11 +144,16 @@ def _run_one_window(samfile, window_start, reference_name, window_length,
         window_start + window_length # arg exclusive as per pysam convention
     )
 
+    # TODO: minimum_overlap
+    # TODO: original_window_length
+    # TODO: window_length
     original_window_length = window_length
+    window_length = control_window_length
     if extended_window_mode:
-        for pos, val in max_ins_at_pos.items():
-            if window_start <= pos < window_start + original_window_length:
-                window_length += val
+        # this is now done intilaly for all windows
+        #for pos, val in max_ins_at_pos.items():
+        #    if window_start <= pos < window_start + original_window_length:
+        #        window_length += val
         minimum_overlap *= window_length/original_window_length
 
     if exclude_non_var_pos_threshold > 0:
@@ -277,7 +282,8 @@ def _run_one_window(samfile, window_start, reference_name, window_length,
     # TODO move out of this function
     convert_to_printed_fmt = lambda x: [f'>{k[0]} {k[1]}\n{"".join(k[2])}' for k in x]
 
-    return convert_to_printed_fmt(arr), arr_read_qualities_summary, arr_read_summary, counter, window_length, pos_filter
+#    return convert_to_printed_fmt(arr), arr_read_qualities_summary, arr_read_summary, counter, window_length, pos_filter
+    return convert_to_printed_fmt(arr), arr_read_qualities_summary, arr_read_summary, pos_filter
 
 
 def parallel_run_one_window(
@@ -288,6 +294,7 @@ def parallel_run_one_window(
     idx,
     window_start,
     window_length,
+    control_window_length,
     alignment_file,
     reference_name,
     win_min_ext,
@@ -315,12 +322,15 @@ def parallel_run_one_window(
 
     logging.info(f"Working on window (1-based) @ {window_start+1}")
 
+#    (arr, arr_read_qualities_summary, arr_read_summary,
+#    counter, control_window_length, pos_filter) = _run_one_window(
     (arr, arr_read_qualities_summary, arr_read_summary,
-     counter, control_window_length, pos_filter) = _run_one_window(
+     pos_filter) = _run_one_window(
         samfile,
         window_start - 1, # make 0 based
         reference_name,
         window_length,
+        control_window_length,
         math.floor(win_min_ext * window_length),
         dict(permitted_reads_per_location), # copys dict ("pass by value")
         counter,
@@ -456,6 +466,32 @@ def parallel_run_one_window(
             )
             _write_to_file([line], f"coverage_{idx}.txt")
 
+
+
+def update_tiling(tiling, extended_window_mode, max_ins_at_pos):
+    """
+    input tiling:
+
+    return: tiling = [
+            (window_start, original_window_length, control_window_length, counter)
+            for each window
+            ]
+    """
+    update_tiling = []
+
+    for idx, (window_start, window_length) in enumerate(tiling):
+        original_window_length = window_length
+        if extended_window_mode:
+            for pos, val in max_ins_at_pos.items():
+                if window_start <= pos < window_start + original_window_length:
+                    window_length += val
+            update_tiling.append((window_start,original_window_length, window_length))
+        else:
+            update_tiling.append((window_start,original_window_length, window_length))
+
+    return update_tiling
+
+
 def build_windows(alignment_file: str, tiling_strategy: TilingStrategy,
     win_min_ext: float, maximum_reads: int, minimum_reads: int,
     reference_filename: str,
@@ -508,7 +544,7 @@ def build_windows(alignment_file: str, tiling_strategy: TilingStrategy,
         threads=max_proc #1
     )
     #reffile = pysam.FastaFile(reference_filename) --> we need to read it in each child process
-    counter = 0
+    #counter = 0 #--> counter is now coputed initially for all windows
     reference_name = tiling_strategy.get_reference_name()
     tiling = tiling_strategy.get_window_tilings()
     region_end = tiling_strategy.get_region_end()
@@ -519,8 +555,15 @@ def build_windows(alignment_file: str, tiling_strategy: TilingStrategy,
         maximum_reads
     )
 
+    tiling = update_tiling(tiling, extended_window_mode, max_ins_at_pos)
+
+    # generate counter for each window
+    # counter = window_start - 1 + control_window_length, # make 0 based
+    counter_list = [0] + [window_start- 1 + control_window_length for (window_start, window_length, control_window_length) in tiling]
+
     all_processes = []
-    for idx, (window_start, window_length) in enumerate(tiling):
+    for idx, (window_start, window_length, control_window_length) in enumerate(tiling):
+        counter = counter_list[idx]
         p = Process(
             target=parallel_run_one_window,
             args=(
@@ -531,6 +574,7 @@ def build_windows(alignment_file: str, tiling_strategy: TilingStrategy,
                 idx,
                 window_start,
                 window_length,
+                control_window_length,
                 alignment_file,
                 reference_name,
                 win_min_ext,
@@ -543,12 +587,13 @@ def build_windows(alignment_file: str, tiling_strategy: TilingStrategy,
                 exclude_non_var_pos_threshold,
                 )
             )
-        p.start()
         all_processes.append(p)
 
     for p in all_processes:
-      p.join()
-    print("here after join")
+      p.run()
+
+    #for p in all_processes:
+    #  p.join()
 
     samfile.close()
 

From 17bfca76c8fdf09d3c11da30f9969360148a9bd4 Mon Sep 17 00:00:00 2001
From: LaraFuhrmann <55209716+LaraFuhrmann@users.noreply.github.com>
Date: Fri, 8 Sep 2023 16:38:27 +0200
Subject: [PATCH 03/25] [test] test_run_one_window had to be adapted as it has
 now also the control_window_length as input

---
 tests/test_b2w_mapping.py | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/tests/test_b2w_mapping.py b/tests/test_b2w_mapping.py
index 0fc3b9c..6eab3f7 100644
--- a/tests/test_b2w_mapping.py
+++ b/tests/test_b2w_mapping.py
@@ -326,11 +326,19 @@ def test_run_one_window(mArr, spec, window_length, window_start, extended_window
     mock_dict = mocker.MagicMock()
     mock_dict.__getitem__.return_value = 42
 
+    # added by Lara
+    original_window_length = window_length
+    control_window_length = window_length
+    for pos, val in max_ins_at_pos.items():
+        if window_start <= pos < window_start + original_window_length:
+            control_window_length += val
+
     arr, _, _, _, _, _ = b2w._run_one_window(
         mock_samfile,
         window_start,
         "HXB2-does-not-matter",
         window_length,
+        control_window_length,
         0,
         mock_dict,
         0,
@@ -343,4 +351,4 @@ def test_run_one_window(mArr, spec, window_length, window_start, extended_window
     print(arr)
 
     for idx, el in enumerate(arr):
-        assert el.split("\n")[1] == spec[idx]
\ No newline at end of file
+        assert el.split("\n")[1] == spec[idx]

From b8b2450231670df19b091af2def223926b7a0dd9 Mon Sep 17 00:00:00 2001
From: LaraFuhrmann <55209716+LaraFuhrmann@users.noreply.github.com>
Date: Fri, 8 Sep 2023 16:45:53 +0200
Subject: [PATCH 04/25] [test] test_run_one_window had to be adapted as it has
 now also the control_window_length as input

---
 tests/test_b2w_mapping.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_b2w_mapping.py b/tests/test_b2w_mapping.py
index 6eab3f7..06fc4b5 100644
--- a/tests/test_b2w_mapping.py
+++ b/tests/test_b2w_mapping.py
@@ -329,7 +329,7 @@ def test_run_one_window(mArr, spec, window_length, window_start, extended_window
     # added by Lara
     original_window_length = window_length
     control_window_length = window_length
-    for pos, val in max_ins_at_pos.items():
+    for pos, val in max_indel_at_pos.items():
         if window_start <= pos < window_start + original_window_length:
             control_window_length += val
 

From 9005626fd87fbc88d74a3d259ccb0ad617ef780a Mon Sep 17 00:00:00 2001
From: LaraFuhrmann <55209716+LaraFuhrmann@users.noreply.github.com>
Date: Fri, 8 Sep 2023 17:25:19 +0200
Subject: [PATCH 05/25] [test] correct expected output

---
 tests/test_b2w_mapping.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/test_b2w_mapping.py b/tests/test_b2w_mapping.py
index 06fc4b5..b432897 100644
--- a/tests/test_b2w_mapping.py
+++ b/tests/test_b2w_mapping.py
@@ -333,9 +333,9 @@ def test_run_one_window(mArr, spec, window_length, window_start, extended_window
         if window_start <= pos < window_start + original_window_length:
             control_window_length += val
 
-    arr, _, _, _, _, _ = b2w._run_one_window(
+    arr, _, _, _, = b2w._run_one_window(
         mock_samfile,
-        window_start,
+        window_start, # 0 based
         "HXB2-does-not-matter",
         window_length,
         control_window_length,

From d863bb540a6cd4181046498ed0eed7984e0d0ae4 Mon Sep 17 00:00:00 2001
From: LaraFuhrmann <55209716+LaraFuhrmann@users.noreply.github.com>
Date: Fri, 8 Sep 2023 17:48:04 +0200
Subject: [PATCH 06/25] [test] computation control_window_length

---
 tests/test_b2w_mapping.py | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/tests/test_b2w_mapping.py b/tests/test_b2w_mapping.py
index b432897..a2da540 100644
--- a/tests/test_b2w_mapping.py
+++ b/tests/test_b2w_mapping.py
@@ -329,9 +329,12 @@ def test_run_one_window(mArr, spec, window_length, window_start, extended_window
     # added by Lara
     original_window_length = window_length
     control_window_length = window_length
-    for pos, val in max_indel_at_pos.items():
-        if window_start <= pos < window_start + original_window_length:
-            control_window_length += val
+
+    if extended_window_mode:
+        for pos, val in max_indel_at_pos.items():
+            if window_start <= pos < window_start + original_window_length:
+                control_window_length += val
+        
 
     arr, _, _, _, = b2w._run_one_window(
         mock_samfile,

From 9b5c349f36908988e41cd628a52f85bfde4e3e8c Mon Sep 17 00:00:00 2001
From: LaraFuhrmann <55209716+LaraFuhrmann@users.noreply.github.com>
Date: Mon, 6 Nov 2023 14:53:53 +0100
Subject: [PATCH 07/25] fixed: problem with hash not being deterministic which
 caused problems in the multi-threading, now using a determinisitc version

---
 shorah/b2w.py | 35 +++++++++++++++++++++++++++--------
 1 file changed, 27 insertions(+), 8 deletions(-)

diff --git a/shorah/b2w.py b/shorah/b2w.py
index 8a71874..78a826d 100644
--- a/shorah/b2w.py
+++ b/shorah/b2w.py
@@ -6,6 +6,7 @@
 import logging
 from multiprocessing import Process, Pool, cpu_count
 import os
+import hashlib
 
 def _write_to_file(lines, file_name):
     with open(file_name, "w") as f:
@@ -40,7 +41,8 @@ def _calc_via_pileup(samfile, reference_name, maximum_reads):
                 indel_map.add((
                     pileupread.alignment.query_name, # TODO is unique?
                     pileupread.alignment.reference_start, # TODO is unique?
-                    hash(pileupread.alignment.cigarstring), # TODO is unique?
+                     hashlib.sha1(pileupread.alignment.cigarstring.encode()).hexdigest(),
+                    #hash(pileupread.alignment.cigarstring), # TODO is unique?
                     pileupcolumn.reference_pos,
                     pileupread.indel,
                     pileupread.is_del
@@ -69,6 +71,12 @@ def _build_one_full_read(full_read: list[str], full_qualities: list[int]|list[st
     change_in_reference_space_ins = 0
 
     for name, start, cigar_hash, ref_pos, indel_len, is_del in indel_map:
+        #, "89.6-2108", "89.6-4066", "89.6-2922"
+        if (read_query_name in ["NL43-2382"]) & (name ==read_query_name) & (start==2357):
+            print("name, start, cigar_hash, ref_pos, indel_len, is_del", name, start, cigar_hash, ref_pos, indel_len, is_del)
+            print("full_read_cigar_hash", full_read_cigar_hash, "cigar_hash", cigar_hash)
+            print("first_aligned_pos", first_aligned_pos, "start", start)
+            #print("extended_window_mode", extended_window_mode)
 
         if name == read_query_name and start == first_aligned_pos and cigar_hash == full_read_cigar_hash:
             if indel_len > 0 and is_del == 1:
@@ -195,9 +203,14 @@ def _run_one_window(samfile, window_start, reference_name, window_length,control
                 raise NotImplementedError("CIGAR op code found that is not implemented:", ct[0])
 
         full_read, full_qualities = _build_one_full_read(full_read, full_qualities,
-            read.query_name, hash(read.cigarstring), first_aligned_pos, last_aligned_pos,
+            read.query_name, hashlib.sha1(read.cigarstring.encode()).hexdigest(), first_aligned_pos, last_aligned_pos,
             indel_map, max_ins_at_pos, extended_window_mode, "-")
 
+        #if  (read.query_name == "NL43-1884"):
+        #    print("oooooooooooooooooooooooooo")
+        #    print(read.query_name, hash(read.cigarstring), first_aligned_pos, last_aligned_pos,
+        #    indel_map, max_ins_at_pos, extended_window_mode)
+
         if (first_aligned_pos + minimum_overlap < window_start + 1 + window_length
                 and last_aligned_pos >= window_start + minimum_overlap - 2 # TODO justify 2
                 and len(full_read) >= minimum_overlap):
@@ -238,12 +251,16 @@ def _run_one_window(samfile, window_start, reference_name, window_length,control
                 cut_out_read = (-start_cut_out + num_inserts_left_of_read) * "N" + cut_out_read
                 if full_qualities is not None:
                     cut_out_qualities = (-start_cut_out + num_inserts_left_of_read) * [2] + cut_out_qualities
-            if len(cut_out_read) != window_length:
-                breakpoint()
+
+            #if (read.query_name in ["NL43-2382", "89.6-2108", "89.6-4066", "89.6-2922"]):
+            #    print(
+            #        "read unequal window size",
+            #        read.query_name, first_aligned_pos, cut_out_read, window_start, window_length, read.reference_end, len(cut_out_read)
+            #    )
 
             assert len(cut_out_read) == window_length, (
                 "read unequal window size",
-                read.query_name, first_aligned_pos, cut_out_read, window_start, window_length, read.reference_end
+                read.query_name, first_aligned_pos, cut_out_read, window_start, window_length, read.reference_end, len(cut_out_read)
             )
             if cut_out_qualities is not None:
                 assert len(cut_out_qualities) == window_length, (
@@ -556,6 +573,8 @@ def build_windows(alignment_file: str, tiling_strategy: TilingStrategy,
     )
 
     tiling = update_tiling(tiling, extended_window_mode, max_ins_at_pos)
+    print("indel_map", indel_map)
+
 
     # generate counter for each window
     # counter = window_start - 1 + control_window_length, # make 0 based
@@ -590,10 +609,10 @@ def build_windows(alignment_file: str, tiling_strategy: TilingStrategy,
         all_processes.append(p)
 
     for p in all_processes:
-      p.run()
+      p.start()
 
-    #for p in all_processes:
-    #  p.join()
+    for p in all_processes:
+      p.join()
 
     samfile.close()
 

From 5214a898cbbbf852e778971f9cdfa079eaa4460c Mon Sep 17 00:00:00 2001
From: LaraFuhrmann <55209716+LaraFuhrmann@users.noreply.github.com>
Date: Mon, 6 Nov 2023 14:57:35 +0100
Subject: [PATCH 08/25] clean up

---
 shorah/b2w.py | 19 +------------------
 1 file changed, 1 insertion(+), 18 deletions(-)

diff --git a/shorah/b2w.py b/shorah/b2w.py
index 78a826d..e4b66ff 100644
--- a/shorah/b2w.py
+++ b/shorah/b2w.py
@@ -71,12 +71,6 @@ def _build_one_full_read(full_read: list[str], full_qualities: list[int]|list[st
     change_in_reference_space_ins = 0
 
     for name, start, cigar_hash, ref_pos, indel_len, is_del in indel_map:
-        #, "89.6-2108", "89.6-4066", "89.6-2922"
-        if (read_query_name in ["NL43-2382"]) & (name ==read_query_name) & (start==2357):
-            print("name, start, cigar_hash, ref_pos, indel_len, is_del", name, start, cigar_hash, ref_pos, indel_len, is_del)
-            print("full_read_cigar_hash", full_read_cigar_hash, "cigar_hash", cigar_hash)
-            print("first_aligned_pos", first_aligned_pos, "start", start)
-            #print("extended_window_mode", extended_window_mode)
 
         if name == read_query_name and start == first_aligned_pos and cigar_hash == full_read_cigar_hash:
             if indel_len > 0 and is_del == 1:
@@ -197,7 +191,7 @@ def _run_one_window(samfile, window_start, reference_name, window_length,control
                 if ct_idx != 0 and ct_idx != len(read.cigartuples)-1:
                     raise ValueError("Soft clipping only possible on the edges of a read.")
             elif ct[0] == 5: # 5 = BAM_CHARD_CLIP
-                #logging.debug(f"[b2w] Hard clipping detected in {read.query_name}")
+                #logging.debug(f"[b2w] Hard clipping detected in {read.query_name}") # commented out because this happens too often
                 pass
             else:
                 raise NotImplementedError("CIGAR op code found that is not implemented:", ct[0])
@@ -206,10 +200,6 @@ def _run_one_window(samfile, window_start, reference_name, window_length,control
             read.query_name, hashlib.sha1(read.cigarstring.encode()).hexdigest(), first_aligned_pos, last_aligned_pos,
             indel_map, max_ins_at_pos, extended_window_mode, "-")
 
-        #if  (read.query_name == "NL43-1884"):
-        #    print("oooooooooooooooooooooooooo")
-        #    print(read.query_name, hash(read.cigarstring), first_aligned_pos, last_aligned_pos,
-        #    indel_map, max_ins_at_pos, extended_window_mode)
 
         if (first_aligned_pos + minimum_overlap < window_start + 1 + window_length
                 and last_aligned_pos >= window_start + minimum_overlap - 2 # TODO justify 2
@@ -252,11 +242,6 @@ def _run_one_window(samfile, window_start, reference_name, window_length,control
                 if full_qualities is not None:
                     cut_out_qualities = (-start_cut_out + num_inserts_left_of_read) * [2] + cut_out_qualities
 
-            #if (read.query_name in ["NL43-2382", "89.6-2108", "89.6-4066", "89.6-2922"]):
-            #    print(
-            #        "read unequal window size",
-            #        read.query_name, first_aligned_pos, cut_out_read, window_start, window_length, read.reference_end, len(cut_out_read)
-            #    )
 
             assert len(cut_out_read) == window_length, (
                 "read unequal window size",
@@ -573,8 +558,6 @@ def build_windows(alignment_file: str, tiling_strategy: TilingStrategy,
     )
 
     tiling = update_tiling(tiling, extended_window_mode, max_ins_at_pos)
-    print("indel_map", indel_map)
-
 
     # generate counter for each window
     # counter = window_start - 1 + control_window_length, # make 0 based

From a96928fda4227abd6552ab40e91c2693289c17eb Mon Sep 17 00:00:00 2001
From: LaraFuhrmann <55209716+LaraFuhrmann@users.noreply.github.com>
Date: Mon, 6 Nov 2023 16:06:06 +0100
Subject: [PATCH 09/25] correct indent

---
 shorah/b2w.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/shorah/b2w.py b/shorah/b2w.py
index e4b66ff..f33b16a 100644
--- a/shorah/b2w.py
+++ b/shorah/b2w.py
@@ -41,7 +41,7 @@ def _calc_via_pileup(samfile, reference_name, maximum_reads):
                 indel_map.add((
                     pileupread.alignment.query_name, # TODO is unique?
                     pileupread.alignment.reference_start, # TODO is unique?
-                     hashlib.sha1(pileupread.alignment.cigarstring.encode()).hexdigest(),
+                    hashlib.sha1(pileupread.alignment.cigarstring.encode()).hexdigest(),
                     #hash(pileupread.alignment.cigarstring), # TODO is unique?
                     pileupcolumn.reference_pos,
                     pileupread.indel,

From b344ae1f0d0e9b0fcfca33a339ced75499c30c8d Mon Sep 17 00:00:00 2001
From: LaraFuhrmann <55209716+LaraFuhrmann@users.noreply.github.com>
Date: Mon, 6 Nov 2023 16:06:55 +0100
Subject: [PATCH 10/25] random hash to deterministic hash

---
 tests/test_b2w_mapping.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/tests/test_b2w_mapping.py b/tests/test_b2w_mapping.py
index a2da540..ad5767c 100644
--- a/tests/test_b2w_mapping.py
+++ b/tests/test_b2w_mapping.py
@@ -2,6 +2,7 @@
 import pytest
 from cigar import Cigar
 from shorah import b2w
+import hashlib
 
 class MockAlignedSegment:
     def __init__(self, query_name: str, reference_start: int, query_sequence: str, cigarstring: str):
@@ -35,10 +36,10 @@ def add_indels(self, indels_map):
         cnt = self.reference_start
         for i in self.cigartuples:
             if i[0] == 1: # insert TODO Justify -1
-                indels_map.append((self.query_name, self.reference_start, hash(self.cigarstring), cnt-1, i[1], 0)) # cnt-1
+                indels_map.append((self.query_name, self.reference_start, hashlib.sha1(self.cigarstring.encode()).hexdigest(), cnt-1, i[1], 0)) # cnt-1
             elif i[0] == 2: # del
                 for k in range(i[1]):
-                    indels_map.append((self.query_name, self.reference_start, hash(self.cigarstring), cnt+k, 0, 1))
+                    indels_map.append((self.query_name, self.reference_start, hashlib.sha1(self.cigarstring.encode()).hexdigest(), cnt+k, 0, 1))
                 cnt += i[1]
             else:
                 cnt += i[1]
@@ -334,7 +335,7 @@ def test_run_one_window(mArr, spec, window_length, window_start, extended_window
         for pos, val in max_indel_at_pos.items():
             if window_start <= pos < window_start + original_window_length:
                 control_window_length += val
-        
+
 
     arr, _, _, _, = b2w._run_one_window(
         mock_samfile,

From 6c2f9e56999b63d3d92c3be079ee049e7092217a Mon Sep 17 00:00:00 2001
From: LaraFuhrmann <55209716+LaraFuhrmann@users.noreply.github.com>
Date: Mon, 6 Nov 2023 16:55:09 +0100
Subject: [PATCH 11/25] update multiprocessing modules that are needed

---
 shorah/b2w.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/shorah/b2w.py b/shorah/b2w.py
index f33b16a..a5dc4e4 100644
--- a/shorah/b2w.py
+++ b/shorah/b2w.py
@@ -4,7 +4,7 @@
 import numpy as np
 import math
 import logging
-from multiprocessing import Process, Pool, cpu_count
+from multiprocessing import Process, cpu_count
 import os
 import hashlib
 

From e6c5e52502e7ae48e54004778e1582d35f77b573 Mon Sep 17 00:00:00 2001
From: LaraFuhrmann <55209716+LaraFuhrmann@users.noreply.github.com>
Date: Thu, 9 Nov 2023 10:52:02 +0100
Subject: [PATCH 12/25] fix: computation control window length

---
 shorah/b2w.py | 24 +++++++++++++-----------
 1 file changed, 13 insertions(+), 11 deletions(-)

diff --git a/shorah/b2w.py b/shorah/b2w.py
index a5dc4e4..10fac02 100644
--- a/shorah/b2w.py
+++ b/shorah/b2w.py
@@ -473,25 +473,27 @@ def parallel_run_one_window(
 def update_tiling(tiling, extended_window_mode, max_ins_at_pos):
     """
     input tiling:
+    window_start is 1-based
+    max_ins_at_pos is 0-based
 
     return: tiling = [
-            (window_start, original_window_length, control_window_length, counter)
+            (window_start, original_window_length, control_window_length)
             for each window
             ]
     """
-    update_tiling = []
+    updated_tiling = []
 
     for idx, (window_start, window_length) in enumerate(tiling):
         original_window_length = window_length
         if extended_window_mode:
             for pos, val in max_ins_at_pos.items():
-                if window_start <= pos < window_start + original_window_length:
+                if window_start - 1 <= pos < window_start - 1 + original_window_length:
                     window_length += val
-            update_tiling.append((window_start,original_window_length, window_length))
+            updated_tiling.append((window_start,original_window_length, window_length))
         else:
-            update_tiling.append((window_start,original_window_length, window_length))
+            updated_tiling.append((window_start,original_window_length, window_length))
 
-    return update_tiling
+    return updated_tiling
 
 
 def build_windows(alignment_file: str, tiling_strategy: TilingStrategy,
@@ -558,10 +560,10 @@ def build_windows(alignment_file: str, tiling_strategy: TilingStrategy,
     )
 
     tiling = update_tiling(tiling, extended_window_mode, max_ins_at_pos)
-
+    
     # generate counter for each window
     # counter = window_start - 1 + control_window_length, # make 0 based
-    counter_list = [0] + [window_start- 1 + control_window_length for (window_start, window_length, control_window_length) in tiling]
+    counter_list = [0] + [window_start - 1 + control_window_length for (window_start, window_length, control_window_length) in tiling]
 
     all_processes = []
     for idx, (window_start, window_length, control_window_length) in enumerate(tiling):
@@ -574,17 +576,17 @@ def build_windows(alignment_file: str, tiling_strategy: TilingStrategy,
                 tiling,
                 region_end,
                 idx,
-                window_start,
+                window_start, # 1-based
                 window_length,
                 control_window_length,
                 alignment_file,
                 reference_name,
                 win_min_ext,
                 permitted_reads_per_location,
-                counter,
+                counter, # 0-based
                 exact_conformance_fix_0_1_basing_in_reads,
                 indel_map,
-                max_ins_at_pos,
+                max_ins_at_pos, # 0-based
                 extended_window_mode,
                 exclude_non_var_pos_threshold,
                 )

From 44b66e42b1b22cf25931c78ab16ae5e291b5b43a Mon Sep 17 00:00:00 2001
From: LaraFuhrmann <55209716+LaraFuhrmann@users.noreply.github.com>
Date: Wed, 22 Nov 2023 17:18:59 +0100
Subject: [PATCH 13/25] delete empty log file

---
 .../learn_error_params/run_dpm_mfa.py                       | 6 +-----
 .../use_quality_scores/run_dpm_mfa.py                       | 6 +-----
 2 files changed, 2 insertions(+), 10 deletions(-)

diff --git a/shorah/local_haplotype_inference/learn_error_params/run_dpm_mfa.py b/shorah/local_haplotype_inference/learn_error_params/run_dpm_mfa.py
index 29332f4..d8dfaac 100644
--- a/shorah/local_haplotype_inference/learn_error_params/run_dpm_mfa.py
+++ b/shorah/local_haplotype_inference/learn_error_params/run_dpm_mfa.py
@@ -10,10 +10,6 @@
 from . import analyze_results
 from . import cavi
 
-logging.basicConfig(
-    filename="shorah_inference.log", encoding="utf-8", level=logging.INFO
-)
-
 
 def gzip_file(f_name):
     """Gzip a file and return the name of the gzipped, removing the original"""
@@ -69,7 +65,7 @@ def main(freads_in, fref_in, output_dir, n_starts, K, alpha0, alphabet="ACGT-",
             0,
             output_name,
         )]
-    
+
     logging.info("len(result_list) " + str(len(result_list)))
     logging.info("reference " + fref_in)
     logging.info("reads " + freads_in)
diff --git a/shorah/local_haplotype_inference/use_quality_scores/run_dpm_mfa.py b/shorah/local_haplotype_inference/use_quality_scores/run_dpm_mfa.py
index 552f228..bffaea5 100644
--- a/shorah/local_haplotype_inference/use_quality_scores/run_dpm_mfa.py
+++ b/shorah/local_haplotype_inference/use_quality_scores/run_dpm_mfa.py
@@ -12,10 +12,6 @@
 from . import analyze_results
 from . import cavi
 
-logging.basicConfig(
-    filename="shorah_inference.log", encoding="utf-8", level=logging.INFO
-)
-
 
 # class NumpyEncoder(json.JSONEncoder):
 #     def default(self, obj):
@@ -96,7 +92,7 @@ def main(
     ]
     # sort list of tuple by ELBO value
     sort_elbo.sort(key=lambda x: x[1], reverse=True)
-    
+
     best_run_idx = sort_elbo[0][0]
     best_run_elbo = sort_elbo[0][1]
     logging.info("Maximal ELBO " + str(best_run_elbo) + "in run " + str(best_run_idx))

From 1ad89510e51e8fd88f45bae43e9c7d2d58689a68 Mon Sep 17 00:00:00 2001
From: LaraFuhrmann <55209716+LaraFuhrmann@users.noreply.github.com>
Date: Wed, 22 Nov 2023 17:21:40 +0100
Subject: [PATCH 14/25] delete empty log file

---
 .../learn_error_params/run_dpm_mfa.py                         | 4 ++++
 .../use_quality_scores/run_dpm_mfa.py                         | 4 ++++
 2 files changed, 8 insertions(+)

diff --git a/shorah/local_haplotype_inference/learn_error_params/run_dpm_mfa.py b/shorah/local_haplotype_inference/learn_error_params/run_dpm_mfa.py
index d8dfaac..62e9952 100644
--- a/shorah/local_haplotype_inference/learn_error_params/run_dpm_mfa.py
+++ b/shorah/local_haplotype_inference/learn_error_params/run_dpm_mfa.py
@@ -10,6 +10,10 @@
 from . import analyze_results
 from . import cavi
 
+logging.basicConfig(
+    filename="viloca.log", encoding="utf-8", level=logging.INFO
+)
+
 
 def gzip_file(f_name):
     """Gzip a file and return the name of the gzipped, removing the original"""
diff --git a/shorah/local_haplotype_inference/use_quality_scores/run_dpm_mfa.py b/shorah/local_haplotype_inference/use_quality_scores/run_dpm_mfa.py
index bffaea5..562f871 100644
--- a/shorah/local_haplotype_inference/use_quality_scores/run_dpm_mfa.py
+++ b/shorah/local_haplotype_inference/use_quality_scores/run_dpm_mfa.py
@@ -12,6 +12,10 @@
 from . import analyze_results
 from . import cavi
 
+logging.basicConfig(
+    filename="viloca.log", encoding="utf-8", level=logging.INFO
+)
+
 
 # class NumpyEncoder(json.JSONEncoder):
 #     def default(self, obj):

From caeded9c20ba5907055e187aa1c6c2924eb6e21b Mon Sep 17 00:00:00 2001
From: LaraFuhrmann <55209716+LaraFuhrmann@users.noreply.github.com>
Date: Wed, 22 Nov 2023 17:29:32 +0100
Subject: [PATCH 15/25] shotgun command to run command

---
 shorah/cli.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/shorah/cli.py b/shorah/cli.py
index de7caf1..bcfedc1 100644
--- a/shorah/cli.py
+++ b/shorah/cli.py
@@ -89,13 +89,13 @@ def snv_run(args):
 def main():
     """Parse command line, run default functions."""
         # logging configuration
-    logging.basicConfig(filename='shorah.log', level=logging.DEBUG,
+    logging.basicConfig(filename='viloca.log', level=logging.DEBUG,
                         format='%(levelname)s %(asctime)s %(filename)s: %(funcName)s() %(lineno)d: \t%(message)s',
                         datefmt='%Y/%m/%d %H:%M:%S',
                         force=True)
 
     logging.info(' '.join(sys.argv))
-    logging.info('shorah version:%s', __version__)
+    logging.info('viloca version:%s', __version__)
 
     # parse command line
     # create the top-level parser
@@ -151,7 +151,7 @@ def main():
 
     parser = argparse.ArgumentParser(
         usage='%(prog)s <subcommand> [options]',
-        epilog="Run `shorah subcommand -h` for more help",
+        epilog="Run `viloca subcommand -h` for more help",
         parents=[version_parser])
 
     subparsers = parser.add_subparsers(
@@ -159,7 +159,7 @@ def main():
 
     # create the parser for command "shotgun"
     parser_shotgun = subparsers.add_parser(
-        'shotgun', help='run local analysis in shotgun mode', parents=[version_parser, parent_parser, coverage_parser])
+        'run', help='run viloca', parents=[version_parser, parent_parser, coverage_parser])
 
     parser_shotgun.add_argument("-w", "--windowsize", metavar='INT',
                                 required=False, type=int, dest="w", default=201, help="window size")

From f15d199c41a2f26fed8d06577b2f7c8671f7999c Mon Sep 17 00:00:00 2001
From: LaraFuhrmann <55209716+LaraFuhrmann@users.noreply.github.com>
Date: Wed, 22 Nov 2023 17:29:57 +0100
Subject: [PATCH 16/25] update log file naming

---
 .../local_haplotype_inference/learn_error_params/run_dpm_mfa.py | 2 +-
 .../local_haplotype_inference/use_quality_scores/run_dpm_mfa.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/shorah/local_haplotype_inference/learn_error_params/run_dpm_mfa.py b/shorah/local_haplotype_inference/learn_error_params/run_dpm_mfa.py
index 62e9952..a66e988 100644
--- a/shorah/local_haplotype_inference/learn_error_params/run_dpm_mfa.py
+++ b/shorah/local_haplotype_inference/learn_error_params/run_dpm_mfa.py
@@ -11,7 +11,7 @@
 from . import cavi
 
 logging.basicConfig(
-    filename="viloca.log", encoding="utf-8", level=logging.INFO
+    filename="viloca_inference.log", encoding="utf-8", level=logging.INFO
 )
 
 
diff --git a/shorah/local_haplotype_inference/use_quality_scores/run_dpm_mfa.py b/shorah/local_haplotype_inference/use_quality_scores/run_dpm_mfa.py
index 562f871..27285ab 100644
--- a/shorah/local_haplotype_inference/use_quality_scores/run_dpm_mfa.py
+++ b/shorah/local_haplotype_inference/use_quality_scores/run_dpm_mfa.py
@@ -13,7 +13,7 @@
 from . import cavi
 
 logging.basicConfig(
-    filename="viloca.log", encoding="utf-8", level=logging.INFO
+    filename="viloca_inference.log", encoding="utf-8", level=logging.INFO
 )
 
 

From 211461c871aefbfb007b8f9f4307f4cc3f2ef123 Mon Sep 17 00:00:00 2001
From: LaraFuhrmann <55209716+LaraFuhrmann@users.noreply.github.com>
Date: Thu, 23 Nov 2023 11:51:41 +0100
Subject: [PATCH 17/25] [README] add channels to conda enviroment installation]

---
 README.md | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index 3c25d77..dcb9af7 100755
--- a/README.md
+++ b/README.md
@@ -1,8 +1,8 @@
 VILOCA: VIral LOcal haplotype reconstruction and mutation CAlling for short and long read data
 ===============
-[![Build Status](https://travis-ci.org/cbg-ethz/shorah.svg?branch=master)](https://travis-ci.org/cbg-ethz/shorah)
-[![Bioconda package](https://img.shields.io/conda/dn/bioconda/shorah.svg?label=Bioconda)](https://bioconda.github.io/recipes/shorah/README.html)
-[![Docker container](https://quay.io/repository/biocontainers/shorah/status)](https://quay.io/repository/biocontainers/shorah)
+[![Build Status](https://travis-ci.org/cbg-ethz/shorah.svg?branch=master)](https://travis-ci.org/cbg-ethz/viloca)
+[![Bioconda package](https://img.shields.io/conda/dn/bioconda/shorah.svg?label=Bioconda)](https://bioconda.github.io/recipes/viloca/README.html)
+[![Docker container](https://quay.io/repository/biocontainers/shorah/status)](https://quay.io/repository/biocontainers/viloca)
 
 
 VILOCA is an open source project for the analysis of next generation sequencing
@@ -17,7 +17,7 @@ genetic variants present in a mixed sample.
 For installation miniconda is recommended: https://docs.conda.io/en/latest/miniconda.html.
 We recommend to install VILOCA in a clean conda environment:
 ```
-conda create --name env_viloca libshorah
+conda create --name env_viloca --channel conda-forge --channel bioconda libshorah
 conda activate env_viloca
 pip install git+https://github.com/LaraFuhrmann/VILOCA@master
 ```

From 956af67047b7ae1c8ba01f34d0fa98d92d613f8d Mon Sep 17 00:00:00 2001
From: LaraFuhrmann <55209716+LaraFuhrmann@users.noreply.github.com>
Date: Thu, 23 Nov 2023 14:40:58 +0100
Subject: [PATCH 18/25] updated readme with new commands

---
 README.md                                                 | 8 ++++----
 {shorah => viloca}/__init__.py                            | 0
 {shorah => viloca}/__main__.py                            | 0
 {shorah => viloca}/b2w.py                                 | 0
 {shorah => viloca}/cli.py                                 | 0
 {shorah => viloca}/envp_post.py                           | 0
 .../learn_error_params/__init__.py                        | 0
 .../learn_error_params/analyze_results.py                 | 0
 .../local_haplotype_inference/learn_error_params/cavi.py  | 0
 .../learn_error_params/elbo_eqs.py                        | 0
 .../learn_error_params/initialization.py                  | 0
 .../learn_error_params/preparation.py                     | 0
 .../learn_error_params/run_dpm_mfa.py                     | 0
 .../learn_error_params/update_eqs.py                      | 0
 .../use_quality_scores/__init__.py                        | 0
 .../use_quality_scores/analyze_results.py                 | 0
 .../local_haplotype_inference/use_quality_scores/cavi.py  | 0
 .../use_quality_scores/elbo_eqs.py                        | 0
 .../use_quality_scores/initialization.py                  | 0
 .../use_quality_scores/preparation.py                     | 0
 .../use_quality_scores/run_dpm_mfa.py                     | 0
 .../use_quality_scores/update_eqs.py                      | 0
 {shorah => viloca}/pooled_post.py                         | 0
 {shorah => viloca}/pooled_pre.py                          | 0
 {shorah => viloca}/shorah_snv.py                          | 0
 {shorah => viloca}/shotgun.py                             | 0
 {shorah => viloca}/tiling.py                              | 0
 27 files changed, 4 insertions(+), 4 deletions(-)
 rename {shorah => viloca}/__init__.py (100%)
 rename {shorah => viloca}/__main__.py (100%)
 rename {shorah => viloca}/b2w.py (100%)
 rename {shorah => viloca}/cli.py (100%)
 rename {shorah => viloca}/envp_post.py (100%)
 rename {shorah => viloca}/local_haplotype_inference/learn_error_params/__init__.py (100%)
 rename {shorah => viloca}/local_haplotype_inference/learn_error_params/analyze_results.py (100%)
 rename {shorah => viloca}/local_haplotype_inference/learn_error_params/cavi.py (100%)
 rename {shorah => viloca}/local_haplotype_inference/learn_error_params/elbo_eqs.py (100%)
 rename {shorah => viloca}/local_haplotype_inference/learn_error_params/initialization.py (100%)
 rename {shorah => viloca}/local_haplotype_inference/learn_error_params/preparation.py (100%)
 rename {shorah => viloca}/local_haplotype_inference/learn_error_params/run_dpm_mfa.py (100%)
 rename {shorah => viloca}/local_haplotype_inference/learn_error_params/update_eqs.py (100%)
 rename {shorah => viloca}/local_haplotype_inference/use_quality_scores/__init__.py (100%)
 rename {shorah => viloca}/local_haplotype_inference/use_quality_scores/analyze_results.py (100%)
 rename {shorah => viloca}/local_haplotype_inference/use_quality_scores/cavi.py (100%)
 rename {shorah => viloca}/local_haplotype_inference/use_quality_scores/elbo_eqs.py (100%)
 rename {shorah => viloca}/local_haplotype_inference/use_quality_scores/initialization.py (100%)
 rename {shorah => viloca}/local_haplotype_inference/use_quality_scores/preparation.py (100%)
 rename {shorah => viloca}/local_haplotype_inference/use_quality_scores/run_dpm_mfa.py (100%)
 rename {shorah => viloca}/local_haplotype_inference/use_quality_scores/update_eqs.py (100%)
 rename {shorah => viloca}/pooled_post.py (100%)
 rename {shorah => viloca}/pooled_pre.py (100%)
 rename {shorah => viloca}/shorah_snv.py (100%)
 rename {shorah => viloca}/shotgun.py (100%)
 rename {shorah => viloca}/tiling.py (100%)

diff --git a/README.md b/README.md
index dcb9af7..7ffafbe 100755
--- a/README.md
+++ b/README.md
@@ -19,20 +19,20 @@ We recommend to install VILOCA in a clean conda environment:
 ```
 conda create --name env_viloca --channel conda-forge --channel bioconda libshorah
 conda activate env_viloca
-pip install git+https://github.com/LaraFuhrmann/VILOCA@master
+pip install git+https://github.com/cbg-ethz/VILOCA@master
 ```
 
 ### Example
 To test your installation, we recommend running the program on `tests/data_1`.
 
 If the sequencing amplicon strategy is known, we recommend using the amplicon-mode of the program, which takes as input the `<smth>.insert.bed` - file:
-`shorah shotgun -b test_aln.cram -f test_ref.fasta -z scheme.insert.bed --mode use_quality_scores`
+`viloca run -b test_aln.cram -f test_ref.fasta -z scheme.insert.bed --mode use_quality_scores`
 
 If the sequencing quality scores are not trustable, the sequencing error parameters can also be learned:
-`shorah shotgun -b test_aln.cram -f test_ref.fasta -z scheme.insert.bed --mode learn_error_params`.
+`viloca run -b test_aln.cram -f test_ref.fasta -z scheme.insert.bed --mode learn_error_params`.
 
 If there is no information on the sequencing amplicon strategy available, run:
-`shorah shotgun -b test_aln.cram -f test_ref.fasta --mode use_quality_scores`
+`viloca run -b test_aln.cram -f test_ref.fasta --mode use_quality_scores`
 
 ### Parameters
 There are several parameters available:  
diff --git a/shorah/__init__.py b/viloca/__init__.py
similarity index 100%
rename from shorah/__init__.py
rename to viloca/__init__.py
diff --git a/shorah/__main__.py b/viloca/__main__.py
similarity index 100%
rename from shorah/__main__.py
rename to viloca/__main__.py
diff --git a/shorah/b2w.py b/viloca/b2w.py
similarity index 100%
rename from shorah/b2w.py
rename to viloca/b2w.py
diff --git a/shorah/cli.py b/viloca/cli.py
similarity index 100%
rename from shorah/cli.py
rename to viloca/cli.py
diff --git a/shorah/envp_post.py b/viloca/envp_post.py
similarity index 100%
rename from shorah/envp_post.py
rename to viloca/envp_post.py
diff --git a/shorah/local_haplotype_inference/learn_error_params/__init__.py b/viloca/local_haplotype_inference/learn_error_params/__init__.py
similarity index 100%
rename from shorah/local_haplotype_inference/learn_error_params/__init__.py
rename to viloca/local_haplotype_inference/learn_error_params/__init__.py
diff --git a/shorah/local_haplotype_inference/learn_error_params/analyze_results.py b/viloca/local_haplotype_inference/learn_error_params/analyze_results.py
similarity index 100%
rename from shorah/local_haplotype_inference/learn_error_params/analyze_results.py
rename to viloca/local_haplotype_inference/learn_error_params/analyze_results.py
diff --git a/shorah/local_haplotype_inference/learn_error_params/cavi.py b/viloca/local_haplotype_inference/learn_error_params/cavi.py
similarity index 100%
rename from shorah/local_haplotype_inference/learn_error_params/cavi.py
rename to viloca/local_haplotype_inference/learn_error_params/cavi.py
diff --git a/shorah/local_haplotype_inference/learn_error_params/elbo_eqs.py b/viloca/local_haplotype_inference/learn_error_params/elbo_eqs.py
similarity index 100%
rename from shorah/local_haplotype_inference/learn_error_params/elbo_eqs.py
rename to viloca/local_haplotype_inference/learn_error_params/elbo_eqs.py
diff --git a/shorah/local_haplotype_inference/learn_error_params/initialization.py b/viloca/local_haplotype_inference/learn_error_params/initialization.py
similarity index 100%
rename from shorah/local_haplotype_inference/learn_error_params/initialization.py
rename to viloca/local_haplotype_inference/learn_error_params/initialization.py
diff --git a/shorah/local_haplotype_inference/learn_error_params/preparation.py b/viloca/local_haplotype_inference/learn_error_params/preparation.py
similarity index 100%
rename from shorah/local_haplotype_inference/learn_error_params/preparation.py
rename to viloca/local_haplotype_inference/learn_error_params/preparation.py
diff --git a/shorah/local_haplotype_inference/learn_error_params/run_dpm_mfa.py b/viloca/local_haplotype_inference/learn_error_params/run_dpm_mfa.py
similarity index 100%
rename from shorah/local_haplotype_inference/learn_error_params/run_dpm_mfa.py
rename to viloca/local_haplotype_inference/learn_error_params/run_dpm_mfa.py
diff --git a/shorah/local_haplotype_inference/learn_error_params/update_eqs.py b/viloca/local_haplotype_inference/learn_error_params/update_eqs.py
similarity index 100%
rename from shorah/local_haplotype_inference/learn_error_params/update_eqs.py
rename to viloca/local_haplotype_inference/learn_error_params/update_eqs.py
diff --git a/shorah/local_haplotype_inference/use_quality_scores/__init__.py b/viloca/local_haplotype_inference/use_quality_scores/__init__.py
similarity index 100%
rename from shorah/local_haplotype_inference/use_quality_scores/__init__.py
rename to viloca/local_haplotype_inference/use_quality_scores/__init__.py
diff --git a/shorah/local_haplotype_inference/use_quality_scores/analyze_results.py b/viloca/local_haplotype_inference/use_quality_scores/analyze_results.py
similarity index 100%
rename from shorah/local_haplotype_inference/use_quality_scores/analyze_results.py
rename to viloca/local_haplotype_inference/use_quality_scores/analyze_results.py
diff --git a/shorah/local_haplotype_inference/use_quality_scores/cavi.py b/viloca/local_haplotype_inference/use_quality_scores/cavi.py
similarity index 100%
rename from shorah/local_haplotype_inference/use_quality_scores/cavi.py
rename to viloca/local_haplotype_inference/use_quality_scores/cavi.py
diff --git a/shorah/local_haplotype_inference/use_quality_scores/elbo_eqs.py b/viloca/local_haplotype_inference/use_quality_scores/elbo_eqs.py
similarity index 100%
rename from shorah/local_haplotype_inference/use_quality_scores/elbo_eqs.py
rename to viloca/local_haplotype_inference/use_quality_scores/elbo_eqs.py
diff --git a/shorah/local_haplotype_inference/use_quality_scores/initialization.py b/viloca/local_haplotype_inference/use_quality_scores/initialization.py
similarity index 100%
rename from shorah/local_haplotype_inference/use_quality_scores/initialization.py
rename to viloca/local_haplotype_inference/use_quality_scores/initialization.py
diff --git a/shorah/local_haplotype_inference/use_quality_scores/preparation.py b/viloca/local_haplotype_inference/use_quality_scores/preparation.py
similarity index 100%
rename from shorah/local_haplotype_inference/use_quality_scores/preparation.py
rename to viloca/local_haplotype_inference/use_quality_scores/preparation.py
diff --git a/shorah/local_haplotype_inference/use_quality_scores/run_dpm_mfa.py b/viloca/local_haplotype_inference/use_quality_scores/run_dpm_mfa.py
similarity index 100%
rename from shorah/local_haplotype_inference/use_quality_scores/run_dpm_mfa.py
rename to viloca/local_haplotype_inference/use_quality_scores/run_dpm_mfa.py
diff --git a/shorah/local_haplotype_inference/use_quality_scores/update_eqs.py b/viloca/local_haplotype_inference/use_quality_scores/update_eqs.py
similarity index 100%
rename from shorah/local_haplotype_inference/use_quality_scores/update_eqs.py
rename to viloca/local_haplotype_inference/use_quality_scores/update_eqs.py
diff --git a/shorah/pooled_post.py b/viloca/pooled_post.py
similarity index 100%
rename from shorah/pooled_post.py
rename to viloca/pooled_post.py
diff --git a/shorah/pooled_pre.py b/viloca/pooled_pre.py
similarity index 100%
rename from shorah/pooled_pre.py
rename to viloca/pooled_pre.py
diff --git a/shorah/shorah_snv.py b/viloca/shorah_snv.py
similarity index 100%
rename from shorah/shorah_snv.py
rename to viloca/shorah_snv.py
diff --git a/shorah/shotgun.py b/viloca/shotgun.py
similarity index 100%
rename from shorah/shotgun.py
rename to viloca/shotgun.py
diff --git a/shorah/tiling.py b/viloca/tiling.py
similarity index 100%
rename from shorah/tiling.py
rename to viloca/tiling.py

From f9e7cb4f45eaaae35d0304751afd3c9434a2a058 Mon Sep 17 00:00:00 2001
From: LaraFuhrmann <55209716+LaraFuhrmann@users.noreply.github.com>
Date: Thu, 23 Nov 2023 14:42:00 +0100
Subject: [PATCH 19/25] update imported packages to viloca, and other naming

---
 viloca/__main__.py |  2 +-
 viloca/b2w.py      |  4 ++--
 viloca/cli.py      | 10 +++++-----
 3 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/viloca/__main__.py b/viloca/__main__.py
index 42e6c65..50ed2a3 100644
--- a/viloca/__main__.py
+++ b/viloca/__main__.py
@@ -8,7 +8,7 @@
 - https://docs.python.org/2/using/cmdline.html#cmdoption-m
 - https://docs.python.org/3/using/cmdline.html#cmdoption-m
 """
-from shorah.cli import main
+from viloca.cli import main
 
 if __name__ == "__main__":
     main()
diff --git a/viloca/b2w.py b/viloca/b2w.py
index 10fac02..505dd9a 100644
--- a/viloca/b2w.py
+++ b/viloca/b2w.py
@@ -1,6 +1,6 @@
 import pysam
 from typing import Optional
-from shorah.tiling import TilingStrategy, EquispacedTilingStrategy
+from viloca.tiling import TilingStrategy, EquispacedTilingStrategy
 import numpy as np
 import math
 import logging
@@ -560,7 +560,7 @@ def build_windows(alignment_file: str, tiling_strategy: TilingStrategy,
     )
 
     tiling = update_tiling(tiling, extended_window_mode, max_ins_at_pos)
-    
+
     # generate counter for each window
     # counter = window_start - 1 + control_window_length, # make 0 based
     counter_list = [0] + [window_start - 1 + control_window_length for (window_start, window_length, control_window_length) in tiling]
diff --git a/viloca/cli.py b/viloca/cli.py
index bcfedc1..902ebd9 100644
--- a/viloca/cli.py
+++ b/viloca/cli.py
@@ -39,12 +39,12 @@
 import argparse
 import logging
 import logging.handlers
-from shorah import shotgun, shorah_snv
+from viloca import shotgun, shorah_snv
 
 # FIXME can we remove this? @Ivan -> version tag (get through poetry in the future)
 use_pkg_resources = False
 all_dirs = os.path.abspath(__file__).split(os.sep)
-base_dir = os.sep.join(all_dirs[:-all_dirs[::-1].index('shorah')])
+base_dir = os.sep.join(all_dirs[:-all_dirs[::-1].index('viloca')])
 version_fname = os.path.join(base_dir, '.version')
 if os.path.exists(version_fname):
     # probably installed using Autotools, e.g: bioconda package - the current recommended way
@@ -54,7 +54,7 @@
     # probably installed using setup.py
     from pkg_resources import (get_distribution, DistributionNotFound)
     try:
-        __version__ = get_distribution('shorah').version
+        __version__ = get_distribution('viloca').version
     except DistributionNotFound:
         __version__ = 'unknown'
         print("cannot find version", file=sys.stderr)
@@ -66,8 +66,8 @@
 if __name__ == '__main__':
     if __package__ is None:
         os.sys.path.insert(1, parent_dir)
-        mod = __import__('shorah')
-        sys.modules["shorah"] = mod
+        mod = __import__('viloca')
+        sys.modules["viloca"] = mod
         #from common import hcv_map, hiv_map, org_dict, wobbles
         #from stats import (genome_coverage, start_stop_coverage)
 # else:

From 9be8f5b780217d49a861c367ea7d9a3ea4d633c1 Mon Sep 17 00:00:00 2001
From: LaraFuhrmann <55209716+LaraFuhrmann@users.noreply.github.com>
Date: Thu, 23 Nov 2023 14:43:18 +0100
Subject: [PATCH 20/25] update viloca naming here

---
 poetry.lock    | 631 +++++++++++++++++++++++++++++++++++++------------
 pyproject.toml |  10 +-
 2 files changed, 485 insertions(+), 156 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index c304ed1..5aa4b8b 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,153 +1,383 @@
+# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
+
 [[package]]
 name = "atomicwrites"
 version = "1.4.1"
 description = "Atomic file writes."
-category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+files = [
+    {file = "atomicwrites-1.4.1.tar.gz", hash = "sha256:81b2c9071a49367a7f770170e5eec8cb66567cfbbc8c73d20ce5ca4a8d71cf11"},
+]
 
 [[package]]
 name = "attrs"
-version = "22.2.0"
+version = "23.1.0"
 description = "Classes Without Boilerplate"
-category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
+files = [
+    {file = "attrs-23.1.0-py3-none-any.whl", hash = "sha256:1f28b4522cdc2fb4256ac1a020c78acf9cba2c6b461ccd2c126f3aa8e8335d04"},
+    {file = "attrs-23.1.0.tar.gz", hash = "sha256:6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015"},
+]
 
 [package.extras]
-cov = ["attrs", "coverage-enable-subprocess", "coverage[toml] (>=5.3)"]
-dev = ["attrs"]
-docs = ["furo", "sphinx", "myst-parser", "zope.interface", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier"]
-tests = ["attrs", "zope.interface"]
-tests-no-zope = ["hypothesis", "pympler", "pytest (>=4.3.0)", "pytest-xdist", "cloudpickle", "mypy (>=0.971,<0.990)", "pytest-mypy-plugins"]
-tests_no_zope = ["hypothesis", "pympler", "pytest (>=4.3.0)", "pytest-xdist", "cloudpickle", "mypy (>=0.971,<0.990)", "pytest-mypy-plugins"]
+cov = ["attrs[tests]", "coverage[toml] (>=5.3)"]
+dev = ["attrs[docs,tests]", "pre-commit"]
+docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"]
+tests = ["attrs[tests-no-zope]", "zope-interface"]
+tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
 
 [[package]]
 name = "bio"
-version = "1.5.3"
+version = "1.6.0"
 description = "bio"
-category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
+files = [
+    {file = "bio-1.6.0-py3-none-any.whl", hash = "sha256:38b14e11625ef233e1a3878c8b13253695e863bd997f94715c248b71612605d5"},
+]
 
 [package.dependencies]
 biopython = ">=1.80"
+gprofiler-official = "*"
 mygene = "*"
+pandas = "*"
+pooch = "*"
 requests = "*"
 tqdm = "*"
 
 [[package]]
 name = "biopython"
-version = "1.80"
+version = "1.81"
 description = "Freely available tools for computational molecular biology."
-category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "biopython-1.81-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:ef7c79b65b0b3f3c7dc59e20a7f8ae5758d8e852cb8b9cace590dc5617e348ba"},
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+    {file = "biopython-1.81-cp310-cp310-win_amd64.whl", hash = "sha256:b37c0d24191e5c96ca02415a5188551980c83a0d518bbc4ffe3c9a5d1fe0ee81"},
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+    {file = "biopython-1.81-cp39-cp39-win32.whl", hash = "sha256:811796f8d222aa3869a50e31e54ce62b69106b47cd8bb06934867c0d843297b5"},
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+    {file = "biopython-1.81.tar.gz", hash = "sha256:2cf38112b6d8415ad39d6a611988cd11fb5f33eb09346666a87263beba9614e0"},
+]
 
 [package.dependencies]
 numpy = "*"
 
 [[package]]
 name = "biothings-client"
-version = "0.2.6"
+version = "0.3.1"
 description = "Python Client for BioThings API services."
-category = "main"
 optional = false
-python-versions = "*"
+python-versions = ">=2.7"
+files = [
+    {file = "biothings_client-0.3.1-py2.py3-none-any.whl", hash = "sha256:c08437f652d9282da785e098288ef7cf3aa2a79f5d90c480eadfce96b846013e"},
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+]
 
 [package.dependencies]
 requests = ">=2.3.0"
 
 [package.extras]
-jsonld = ["PyLD (>=0.7.2)"]
-dataframe = ["pandas (>=0.18.0)"]
 caching = ["requests-cache (>=0.4.13)"]
+dataframe = ["pandas (>=0.18.0)"]
+jsonld = ["PyLD (>=0.7.2)"]
 
 [[package]]
 name = "certifi"
-version = "2022.12.7"
+version = "2023.11.17"
 description = "Python package for providing Mozilla's CA Bundle."
-category = "main"
 optional = false
 python-versions = ">=3.6"
+files = [
+    {file = "certifi-2023.11.17-py3-none-any.whl", hash = "sha256:e036ab49d5b79556f99cfc2d9320b34cfbe5be05c5871b51de9329f0603b0474"},
+    {file = "certifi-2023.11.17.tar.gz", hash = "sha256:9b469f3a900bf28dc19b8cfbf8019bf47f7fdd1a65a1d4ffb98fc14166beb4d1"},
+]
 
 [[package]]
 name = "charset-normalizer"
-version = "2.1.1"
+version = "3.3.2"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
-category = "main"
 optional = false
-python-versions = ">=3.6.0"
-
-[package.extras]
-unicode_backport = ["unicodedata2"]
+python-versions = ">=3.7.0"
+files = [
+    {file = "charset-normalizer-3.3.2.tar.gz", hash = "sha256:f30c3cb33b24454a82faecaf01b19c18562b1e89558fb6c56de4d9118a032fd5"},
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 numpy = [
@@ -160,52 +390,117 @@ pytz = ">=2020.1"
 [package.extras]
 test = ["hypothesis (>=5.5.3)", "pytest (>=6.0)", "pytest-xdist (>=1.31)"]
 
+[[package]]
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 testing = ["pytest", "pytest-benchmark"]
 
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+]
 
 [[package]]
 name = "pytest"
 version = "6.2.5"
 description = "pytest: simple powerful testing with Python"
-category = "dev"
 optional = false
 python-versions = ">=3.6"
+files = [
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+]
 
 [package.dependencies]
 atomicwrites = {version = ">=1.0", markers = "sys_platform == \"win32\""}
@@ -222,193 +517,227 @@ testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "requests", "xm
 
 [[package]]
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-version = "3.10.0"
+version = "3.12.0"
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-category = "dev"
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-python-versions = ">=3.7"
+python-versions = ">=3.8"
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 [package.dependencies]
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 [package.extras]
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+dev = ["pre-commit", "pytest-asyncio", "tox"]
 
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 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
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 [[package]]
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+version = "2023.3.post1"
 description = "World timezone definitions, modern and historical"
-category = "main"
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 [[package]]
 name = "tqdm"
-version = "4.64.1"
+version = "4.66.1"
 description = "Fast, Extensible Progress Meter"
-category = "main"
 optional = false
-python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,>=2.7"
+python-versions = ">=3.7"
+files = [
+    {file = "tqdm-4.66.1-py3-none-any.whl", hash = "sha256:d302b3c5b53d47bce91fea46679d9c3c6508cf6332229aa1e7d8653723793386"},
+    {file = "tqdm-4.66.1.tar.gz", hash = "sha256:d88e651f9db8d8551a62556d3cff9e3034274ca5d66e93197cf2490e2dcb69c7"},
+]
 
 [package.dependencies]
 colorama = {version = "*", markers = "platform_system == \"Windows\""}
 
 [package.extras]
-dev = ["py-make (>=0.1.0)", "twine", "wheel"]
+dev = ["pytest (>=6)", "pytest-cov", "pytest-timeout", "pytest-xdist"]
 notebook = ["ipywidgets (>=6)"]
 slack = ["slack-sdk"]
 telegram = ["requests"]
 
 [[package]]
 name = "urllib3"
-version = "1.26.13"
+version = "2.1.0"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
-category = "main"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
+python-versions = ">=3.8"
+files = [
+    {file = "urllib3-2.1.0-py3-none-any.whl", hash = "sha256:55901e917a5896a349ff771be919f8bd99aff50b79fe58fec595eb37bbc56bb3"},
+    {file = "urllib3-2.1.0.tar.gz", hash = "sha256:df7aa8afb0148fa78488e7899b2c59b5f4ffcfa82e6c54ccb9dd37c1d7b52d54"},
+]
 
 [package.extras]
-brotli = ["brotlicffi (>=0.8.0)", "brotli (>=1.0.9)", "brotlipy (>=0.6.0)"]
-secure = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "certifi", "urllib3-secure-extra", "ipaddress"]
-socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
+brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"]
+socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
+zstd = ["zstandard (>=0.18.0)"]
 
 [metadata]
-lock-version = "1.1"
+lock-version = "2.0"
 python-versions = ">=3.9.9,<3.11"
 content-hash = "97bd296adc5a4e0c9d69f5be058b42eb938c22c8194b35a9ad7aaba90c019c46"
-
-[metadata.files]
-atomicwrites = []
-attrs = []
-bio = []
-biopython = []
-biothings-client = []
-certifi = []
-charset-normalizer = []
-cigar = []
-colorama = []
-idna = []
-iniconfig = []
-mygene = []
-numpy = []
-packaging = []
-pandas = []
-pluggy = [
-    {file = "pluggy-1.0.0-py2.py3-none-any.whl", hash = "sha256:74134bbf457f031a36d68416e1509f34bd5ccc019f0bcc952c7b909d06b37bd3"},
-    {file = "pluggy-1.0.0.tar.gz", hash = "sha256:4224373bacce55f955a878bf9cfa763c1e360858e330072059e10bad68531159"},
-]
-py = [
-    {file = "py-1.11.0-py2.py3-none-any.whl", hash = "sha256:607c53218732647dff4acdfcd50cb62615cedf612e72d1724fb1a0cc6405b378"},
-    {file = "py-1.11.0.tar.gz", hash = "sha256:51c75c4126074b472f746a24399ad32f6053d1b34b68d2fa41e558e6f4a98719"},
-]
-pybind11 = []
-pysam = [
-    {file = "pysam-0.18.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:ef5d8ad01cac8974cd09832c226cbb63a3f7c5bd63727d8e59447021ee16a186"},
-    {file = "pysam-0.18.0-cp310-cp310-manylinux_2_12_i686.manylinux2010_i686.whl", hash = "sha256:ca0c9289dfdc5e1a81bccdb8305192cd14cf9730bd21320ceca949fde071a572"},
-    {file = "pysam-0.18.0-cp310-cp310-manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:e13e496da3a432db24f424439834b0ab5f40700a3db6e610d06f8bd639d9fd2d"},
-    {file = "pysam-0.18.0-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:c90341434e7a99439174aa64ca5406f63528be4217d4401fb30ec4ea4629c559"},
-    {file = "pysam-0.18.0-cp36-cp36m-manylinux_2_12_i686.manylinux2010_i686.whl", hash = "sha256:a88f875114bd3d8efb7fade80e0640094383ec5043861aa575175fa9a56edf90"},
-    {file = "pysam-0.18.0-cp36-cp36m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:7ea2e019294e4bf25e4892b5de69c43f54fb6ac42b681265268aa322e1f36f5b"},
-    {file = "pysam-0.18.0-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:cfb162358c5284b31b2b88b10947e0f1013da2d85ba0fd0b5723dd142c15329e"},
-    {file = "pysam-0.18.0-cp37-cp37m-manylinux_2_12_i686.manylinux2010_i686.whl", hash = "sha256:9422c2d0b581c3d24f247c15bb8981569e636003c4d6cad39ccd1bf205a79f2c"},
-    {file = "pysam-0.18.0-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:cfffad99cf3968cf85aadb70a8a02303f9172ea21abe02d587c44f808c504f52"},
-    {file = "pysam-0.18.0-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:7a8a25fceaaa96e5b4c8b0a7fd6bb0b20b6c262dc4cc867c6d1467ac990f1d77"},
-    {file = "pysam-0.18.0-cp38-cp38-manylinux_2_12_i686.manylinux2010_i686.whl", hash = "sha256:493988420db16e6ee03393518e4d272df05f0a35780248c08c61da7411e520e7"},
-    {file = "pysam-0.18.0-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:7f6a4ec58ad7995b791a71bf35f673ea794e734c587ea7329fca5cce9c53a7af"},
-    {file = "pysam-0.18.0-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:0cfa16f76ed3c3119c7b3c8dfdcba9e010fbcdcf87eaa165351bb369da5a6bf1"},
-    {file = "pysam-0.18.0-cp39-cp39-manylinux_2_12_i686.manylinux2010_i686.whl", hash = "sha256:2717509556fecddf7c73966fa62066c6a59a7d39b755d8972afa8d143a1d5aa5"},
-    {file = "pysam-0.18.0-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:f5a23a5dcf32f01c66d44e89113fa8f7522997ea43fbc0f98e5250a907911a5f"},
-    {file = "pysam-0.18.0.tar.gz", hash = "sha256:1d6d49a0b3c626fae410a93d4c80583a8b5ddaacc9b46a080b250dbcebd30a59"},
-]
-pytest = [
-    {file = "pytest-6.2.5-py3-none-any.whl", hash = "sha256:7310f8d27bc79ced999e760ca304d69f6ba6c6649c0b60fb0e04a4a77cacc134"},
-    {file = "pytest-6.2.5.tar.gz", hash = "sha256:131b36680866a76e6781d13f101efb86cf674ebb9762eb70d3082b6f29889e89"},
-]
-pytest-mock = []
-python-dateutil = [
-    {file = "python-dateutil-2.8.2.tar.gz", hash = "sha256:0123cacc1627ae19ddf3c27a5de5bd67ee4586fbdd6440d9748f8abb483d3e86"},
-    {file = "python_dateutil-2.8.2-py2.py3-none-any.whl", hash = "sha256:961d03dc3453ebbc59dbdea9e4e11c5651520a876d0f4db161e8674aae935da9"},
-]
-pytz = []
-pyyaml = []
-requests = []
-scipy = []
-six = [
-    {file = "six-1.16.0-py2.py3-none-any.whl", hash = "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254"},
-    {file = "six-1.16.0.tar.gz", hash = "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926"},
-]
-toml = [
-    {file = "toml-0.10.2-py2.py3-none-any.whl", hash = "sha256:806143ae5bfb6a3c6e736a764057db0e6a0e05e338b5630894a5f779cabb4f9b"},
-    {file = "toml-0.10.2.tar.gz", hash = "sha256:b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f"},
-]
-tqdm = []
-urllib3 = []
diff --git a/pyproject.toml b/pyproject.toml
index 57fe425..2f7004f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,16 +1,16 @@
 [tool.poetry]
-name = "ShoRAH"
+name = "VILOCA"
 version = "0.1.0"
 description = "SHOrt Reads Assembly into Haplotypes"
 license = "GPL-3.0-only"
-authors = ["Benjamin Langer <blanger@student.ethz.ch>"]
-build = "build.py"
+authors = ["Benjamin Langer <blanger@student.ethz.ch>, Lara Fuhrmann]
+#build = "build.py" # Lara: I am not sure if we need this or not.
 packages = [
-    { include = "shorah" }
+    { include = "viloca" }
 ]
 
 [tool.poetry.scripts]
-shorah = 'shorah.cli:main'
+viloca = 'viloca.cli:main'
 
 [tool.poetry.dependencies]
 python = ">=3.9.9,<3.11"

From 4fe78c8a11c2aba8df4749c587c937c99a460e8f Mon Sep 17 00:00:00 2001
From: LaraFuhrmann <55209716+LaraFuhrmann@users.noreply.github.com>
Date: Thu, 23 Nov 2023 14:43:37 +0100
Subject: [PATCH 21/25] update viloca naming here

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 2f7004f..7a50826 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -3,7 +3,7 @@ name = "VILOCA"
 version = "0.1.0"
 description = "SHOrt Reads Assembly into Haplotypes"
 license = "GPL-3.0-only"
-authors = ["Benjamin Langer <blanger@student.ethz.ch>, Lara Fuhrmann]
+authors = ["Benjamin Langer <blanger@student.ethz.ch>, Lara Fuhrmann"]
 #build = "build.py" # Lara: I am not sure if we need this or not.
 packages = [
     { include = "viloca" }

From 1d4185fbc0ed9c7c35a13906ab0328ae56c73497 Mon Sep 17 00:00:00 2001
From: LaraFuhrmann <55209716+LaraFuhrmann@users.noreply.github.com>
Date: Thu, 23 Nov 2023 14:51:03 +0100
Subject: [PATCH 22/25] [unit tests] update commands

---
 tests/data_1/shotgun_test.sh    | 2 +-
 tests/data_5/shotgun_prepare.sh | 2 +-
 tests/test_b2w.py               | 2 +-
 tests/test_b2w_mapping.py       | 2 +-
 tests/test_envp_post.py         | 2 +-
 tests/test_pooled_post.py       | 4 ++--
 tests/test_pooled_pre.py        | 4 ++--
 tests/test_shorah_snv.py        | 4 ++--
 tests/test_tiling.py            | 2 +-
 9 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/tests/data_1/shotgun_test.sh b/tests/data_1/shotgun_test.sh
index 0ac3749..77925d3 100755
--- a/tests/data_1/shotgun_test.sh
+++ b/tests/data_1/shotgun_test.sh
@@ -1,4 +1,4 @@
 #!/bin/bash
 
-shorah shotgun -a 0.1 -w 201 -x 100000 -p 0.9 -c 0 \
+viloca run -a 0.1 -w 201 -x 100000 -p 0.9 -c 0 \
 -r HXB2:2469-3713 -R 42 -f test_ref.fasta -b test_aln.cram --out_format csv "$@"
diff --git a/tests/data_5/shotgun_prepare.sh b/tests/data_5/shotgun_prepare.sh
index 81564db..0ce7749 100755
--- a/tests/data_5/shotgun_prepare.sh
+++ b/tests/data_5/shotgun_prepare.sh
@@ -1,3 +1,3 @@
 #!/bin/bash
 
-shorah shotgun -a 0.1 -w 42 -x 100000 -p 0.9 -c 0 -r REF:43-273 -R 42 -b test_aln.cram -f ref.fasta
+viloca run -a 0.1 -w 42 -x 100000 -p 0.9 -c 0 -r REF:43-273 -R 42 -b test_aln.cram -f ref.fasta
diff --git a/tests/test_b2w.py b/tests/test_b2w.py
index c41609a..7a3dd8e 100644
--- a/tests/test_b2w.py
+++ b/tests/test_b2w.py
@@ -2,7 +2,7 @@
 import filecmp
 import os
 import glob
-from shorah import b2w, tiling
+from viloca import b2w, tiling
 import math
 import libshorah
 
diff --git a/tests/test_b2w_mapping.py b/tests/test_b2w_mapping.py
index ad5767c..6a0fb84 100644
--- a/tests/test_b2w_mapping.py
+++ b/tests/test_b2w_mapping.py
@@ -1,7 +1,7 @@
 from array import array
 import pytest
 from cigar import Cigar
-from shorah import b2w
+from viloca import b2w
 import hashlib
 
 class MockAlignedSegment:
diff --git a/tests/test_envp_post.py b/tests/test_envp_post.py
index 205ed05..d4b4fb3 100644
--- a/tests/test_envp_post.py
+++ b/tests/test_envp_post.py
@@ -1,5 +1,5 @@
 from unittest.mock import patch, mock_open
-from shorah import envp_post
+from viloca import envp_post
 
 DEFAULT_MOCK_DATA = "default mock data"
 
diff --git a/tests/test_pooled_post.py b/tests/test_pooled_post.py
index f491ba5..7baf31c 100644
--- a/tests/test_pooled_post.py
+++ b/tests/test_pooled_post.py
@@ -1,5 +1,5 @@
 from unittest.mock import patch, mock_open
-from shorah import pooled_post
+from viloca import pooled_post
 import numpy as np
 
 DEFAULT_MOCK_DATA = "default mock data"
@@ -48,4 +48,4 @@ def open_side_effect(name):
 #                                      open("debug/w-HXB2-2938-3138.dbg"),
 #                                      open("support/w-HXB2-2938-3138.reads-support.fas"),
 #                                      open("corrected/w-HXB2-2938-3138.reads-cor.fas"),
-#                                      "shorah") # TODO
\ No newline at end of file
+#                                      "shorah") # TODO
diff --git a/tests/test_pooled_pre.py b/tests/test_pooled_pre.py
index ce36024..dbe59ab 100644
--- a/tests/test_pooled_pre.py
+++ b/tests/test_pooled_pre.py
@@ -1,6 +1,6 @@
 import pysam
 import os
-from shorah import pooled_pre
+from viloca import pooled_pre
 
 def test__annotate_alignment_file():
     out = "out.bam"
@@ -48,4 +48,4 @@ def test_pre_process_pooled():
     os.remove(out + ".bai")
 
     assert a[0] == a[1] != 0
-    assert a[2] == 0
\ No newline at end of file
+    assert a[2] == 0
diff --git a/tests/test_shorah_snv.py b/tests/test_shorah_snv.py
index 56b0166..4967b55 100644
--- a/tests/test_shorah_snv.py
+++ b/tests/test_shorah_snv.py
@@ -1,5 +1,5 @@
 import pytest
-from shorah.shorah_snv import _compare_ref_to_read, SNP_id, SNV
+from viloca.shorah_snv import _compare_ref_to_read, SNP_id, SNV
 
 
 @pytest.mark.parametrize("ref, seq, spec", [
@@ -39,4 +39,4 @@ def test_compare_ref_to_read(ref, seq, spec):
 
     assert snp == spec
 
-    assert tot_snv == len(snp)
\ No newline at end of file
+    assert tot_snv == len(snp)
diff --git a/tests/test_tiling.py b/tests/test_tiling.py
index f44d66f..89e38fc 100644
--- a/tests/test_tiling.py
+++ b/tests/test_tiling.py
@@ -1,4 +1,4 @@
-from shorah import tiling
+from viloca import tiling
 import pytest
 
 def test_equispaced():

From a7ae55968ed51bcbd3ec1a419a27df42b7d3d997 Mon Sep 17 00:00:00 2001
From: LaraFuhrmann <55209716+LaraFuhrmann@users.noreply.github.com>
Date: Thu, 23 Nov 2023 14:54:50 +0100
Subject: [PATCH 23/25] update author

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 7a50826..af80064 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -3,7 +3,7 @@ name = "VILOCA"
 version = "0.1.0"
 description = "SHOrt Reads Assembly into Haplotypes"
 license = "GPL-3.0-only"
-authors = ["Benjamin Langer <blanger@student.ethz.ch>, Lara Fuhrmann"]
+authors = ["Benjamin Langer <blanger@student.ethz.ch>, Lara Fuhrmann <lara.fuhrmann@bsse.ethz.ch>"]
 #build = "build.py" # Lara: I am not sure if we need this or not.
 packages = [
     { include = "viloca" }

From da27b766a92f451476167f5618d9dd6c49320f61 Mon Sep 17 00:00:00 2001
From: LaraFuhrmann <55209716+LaraFuhrmann@users.noreply.github.com>
Date: Thu, 23 Nov 2023 15:00:10 +0100
Subject: [PATCH 24/25] build is needed for libshorah

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index af80064..42da0bd 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ version = "0.1.0"
 description = "SHOrt Reads Assembly into Haplotypes"
 license = "GPL-3.0-only"
 authors = ["Benjamin Langer <blanger@student.ethz.ch>, Lara Fuhrmann <lara.fuhrmann@bsse.ethz.ch>"]
-#build = "build.py" # Lara: I am not sure if we need this or not.
+build = "build.py"
 packages = [
     { include = "viloca" }
 ]

From 98a8e981264052b18a5c15c9cc10dc198d538732 Mon Sep 17 00:00:00 2001
From: LaraFuhrmann <55209716+LaraFuhrmann@users.noreply.github.com>
Date: Mon, 27 Nov 2023 14:19:10 +0100
Subject: [PATCH 25/25] updated readme

---
 README.md | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/README.md b/README.md
index 7ffafbe..412dd01 100755
--- a/README.md
+++ b/README.md
@@ -1,9 +1,5 @@
 VILOCA: VIral LOcal haplotype reconstruction and mutation CAlling for short and long read data
 ===============
-[![Build Status](https://travis-ci.org/cbg-ethz/shorah.svg?branch=master)](https://travis-ci.org/cbg-ethz/viloca)
-[![Bioconda package](https://img.shields.io/conda/dn/bioconda/shorah.svg?label=Bioconda)](https://bioconda.github.io/recipes/viloca/README.html)
-[![Docker container](https://quay.io/repository/biocontainers/shorah/status)](https://quay.io/repository/biocontainers/viloca)
-
 
 VILOCA is an open source project for the analysis of next generation sequencing
 data. It is designed to analyse genetically heterogeneous samples. Its tools
@@ -23,7 +19,11 @@ pip install git+https://github.com/cbg-ethz/VILOCA@master
 ```
 
 ### Example
-To test your installation, we recommend running the program on `tests/data_1`.
+To test your installation run VILOCA `tests/data_1`:
+```
+viloca run -b test_aln.cram -f test_ref.fasta -z scheme.insert.bed --mode use_quality_scores
+```
+
 
 If the sequencing amplicon strategy is known, we recommend using the amplicon-mode of the program, which takes as input the `<smth>.insert.bed` - file:
 `viloca run -b test_aln.cram -f test_ref.fasta -z scheme.insert.bed --mode use_quality_scores`