fixed bam stats bug

jonas-fuchs · Aug 7, 2024 · 95567e9 · 95567e9
1 parent cb4d1f4
commit 95567e9
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Showing 2 changed files with 4 additions and 1 deletion.
diff --git a/bamdash/command.py b/bamdash/command.py
@@ -300,7 +300,7 @@ def main(sysargs=sys.argv[1:]):
  # dump track data
  vcf_track_count, bed_track_count, gb_track_count = 0, 0, 0
  if args.dump:
- pd.DataFrame.from_dict(stat_dict, orient="index").to_csv("bam_stats.tabular", sep="\t", header=False, index=True)
+ pd.DataFrame.from_dict(stat_dict, orient="index").to_csv(f"{args.reference}_bam_stats.tabular", sep="\t", header=False, index=True)
  if track_data:
  for track in track_data:
  if track[1] == "vcf":

diff --git a/bamdash/scripts/data.py b/bamdash/scripts/data.py
@@ -51,6 +51,9 @@ def make_title_string(parsed_bam, coverage_df, reference, min_cov):
  stat_dict = {}
  # get bam stats for correct chrom
  bam_stats = parsed_bam.get_index_statistics()[0]
+ for bam_stats in parsed_bam.get_index_statistics():
+ if bam_stats[0] == reference:
+ break
  # pop dict
  stat_dict["reference"] = bam_stats[0]
  stat_dict["reference length (bp)"] = parsed_bam.get_reference_length(reference)