adding integration test for bit-get-cov-stats; updated changelog

Author: Mike Lee

CHANGELOG.md

@@ -12,11 +12,12 @@
 
 -->
 
-## Not released yet
+## v1.13.4 (20-Nov-2025)
+
 ### Changed
 - updates to `bit-get-cov-stats`
   - can start from bam file now in addition to mosdepth per-base.bed.gz (will generate the mosdepth output if starting from bam)
-  - modularized
+  - modularized, integration test added
 - updates to `bit-check-for-fastq-dup-headers`
   - autodetect gzipped or not
   - modularized, test added

bit/modules/cov_analyzer.py

@@ -123,7 +123,7 @@ def generate_sliding_bed_file(reference_fasta, sliding_window_size, step_size, o
 
 
 def run_mosdepth(bam_file, window_bed_path, output_dir):
-    mosdepth_out_prefix = f"{output_dir}/mosdepth-files/{bam_file[:-4]}"
+    mosdepth_out_prefix = str(Path(output_dir) / Path(bam_file).stem)
     cmd = f"mosdepth --by {window_bed_path} {mosdepth_out_prefix} {bam_file}"
     subprocess.run(cmd, shell=True)
     mosdepth_regions_file = f"{mosdepth_out_prefix}.regions.bed.gz"

bit/modules/get_cov_stats.py

@@ -16,10 +16,8 @@
 def get_cov_stats(args):
 
     preflight_checks(args)
-
     refs = parse_refs(args.reference_fastas)
 
-
     if args.bed:
         refs = parse_bed_file(refs, args.bed)
     else:
@@ -95,7 +93,7 @@ def parse_bed_file(refs, bed_file):
 def run_mosdepth(bam_file, output_prefix):
     check_bam_file_is_indexed(bam_file)
     mosdepth_output_dir = f"{output_prefix}-mosdepth-files"
-    mosdepth_prefix = f"{mosdepth_output_dir}/{bam_file[:-4]}"
+    mosdepth_prefix = str(Path(mosdepth_output_dir) / Path(bam_file).stem)
     os.makedirs(mosdepth_output_dir, exist_ok=True)
     cmd = f"mosdepth {mosdepth_prefix} {bam_file}"
     print(f"\n  {Fore.YELLOW}Running mosdepth to generate the required per-base coverage file...")
@@ -115,7 +113,7 @@ def check_bam_file_is_indexed(bam_file):
 def generate_output(refs, output_prefix):
     primary_out_path = f"{output_prefix}.tsv"
     with open(primary_out_path, "w") as f:
-        f.write("Ref\tDetection\tDetection_at_10x\tAverage_coverage\n")
+        f.write("ref\tdetection\tdetection_at_10x\taverage_coverage\n")
         for ref in refs:
             detection, detection_at_10x, average_coverage = ref.compute_metrics()
             f.write(f"{ref.path}\t{detection}\t{detection_at_10x}\t{average_coverage}\n")

bit/tests/data/ez-screen.bam

@@ -0,0 +1,36 @@
+
+from pathlib import Path
+import pytest
+from bit.modules.general import get_package_path
+from bit.tests.utils import run_cli
+
+test_fasta_path = get_package_path("tests/data/ez-screen-assembly.fasta")
+test_bam_path = get_package_path("tests/data/ez-screen.bam")
+
+def test_get_cov_stats(tmp_path):
+    out_prefix = tmp_path / "cov-stats"
+
+    cmd = [
+        "bit-get-cov-stats",
+        "-r", str(test_fasta_path),
+        "-b", str(test_bam_path),
+        "-o", str(out_prefix),
+    ]
+
+    run_cli(cmd)
+
+    summary_tsv = Path(f"{out_prefix}.tsv")
+    assert summary_tsv.exists(), f"Coverage stats TSV not found at {summary_tsv}"
+
+    observed = summary_tsv.read_text().splitlines()
+    expected_header = "ref\tdetection\tdetection_at_10x\taverage_coverage"
+    assert observed[0] == expected_header, f"Header does not match expected:\n{observed[0]}\nExpected:\n{expected_header}"
+
+    fields = observed[1].split("\t")
+    assert len(fields) == 4, f"Unexpected number of columns:\n{fields}"
+
+    ref, detection, detection10x, avg_cov = fields
+    assert ref.endswith("ez-screen-assembly.fasta"), f"Unexpected ref path: {ref}"
+    assert float(detection) == pytest.approx(0.8714, rel=1e-3)
+    assert float(detection10x) == pytest.approx(0.0, rel=1e-1)
+    assert float(avg_cov) == pytest.approx(1.9934, rel=1e-1)