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fix_vcf_ploidies: bgzip must stay a filter, not take a filename #1989

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Merged
glennhickey merged 1 commit into from
Aug 31, 2026
Merged

fix_vcf_ploidies: bgzip must stay a filter, not take a filename #1989

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5 changes: 4 additions & 1 deletion src/cactus/refmap/cactus_graphmap_join.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2072,7 +2072,10 @@ def signature_ploidies(sig):
out_file.write(b'\t'.join(toks) + b'\n')

if raw_out_path != out_vcf_path:
cactus_call(parameters=['bgzip', raw_out_path, '--threads', str(threads)], infile=raw_out_path,
# no filename argument: bgzip given one compresses in place, writing raw_out_path.gz and
# deleting the original, so out_vcf_path would get an empty stdout and the remove below
# would fail. it has to stay a stdin/stdout filter, as in minigraph_gfa_to_pansn
cactus_call(parameters=['bgzip', '--threads', str(threads)], infile=raw_out_path,
outfile=out_vcf_path)
os.remove(raw_out_path)

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