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bcftools 1.21 compatibility and typo fix in hatchet.ini #234

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bcftools 1.21 compatibility and typo fix in hatchet.ini #234

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8f7fc1f
#227:fix AD to INFO/AD and sp deadlock bug
Nov 22, 2024
ecbd52f
#231:fix hatchet.ini typo
Nov 22, 2024
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2 changes: 1 addition & 1 deletion script/hatchet.ini
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Original file line number Diff line number Diff line change
Expand Up @@ -64,7 +64,7 @@ msr = 5000
# Minimum number of total reads per bin and sample
mtr = 5000

[cluster_bins_loc]
[cluster_bins]
diploidbaf = 0.08
# Minimum and maximum number of clusters to infer
# (using silhouette score for model selection)
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4 changes: 3 additions & 1 deletion src/hatchet/utils/count_alleles.py
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Expand Up @@ -264,7 +264,7 @@ def countAlleles(self, bamfile, samplename, chromosome):
self.dp,
self.snplist[chromosome],
)
cmd_query = "{} query -f '%CHROM\\t%POS\\t%REF,%ALT\\t%AD\\n' -i 'SUM(AD)<={} & SUM(AD)>={}'".format(
cmd_query = "{} query -f '%CHROM\\t%POS\\t%REF,%ALT\\t%AD\\n' -i 'SUM(INFO/AD)<={} & SUM(INFO/AD)>={}'".format(
self.bcftools, self.dp, self.mincov
)
if self.E:
Expand All @@ -287,6 +287,8 @@ def countAlleles(self, bamfile, samplename, chromosome):
stderr=err,
universal_newlines=True,
)
# Allow sp mpileup to receive a SIGPIPE if p2 exits. avoid deadlock
mpileup.stdout.close()
stdout, _ = query.communicate()
codes = map(lambda p: p.wait(), [mpileup, query])
if any(c != 0 for c in codes):
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