#227:fix AD to INFO/AD and sp deadlock bug

raphael-group · Nov 22, 2024 · 8f7fc1f · 8f7fc1f
1 parent 7115c38
commit 8f7fc1f
Showing 1 changed file with 3 additions and 1 deletion.
diff --git a/src/hatchet/utils/count_alleles.py b/src/hatchet/utils/count_alleles.py
@@ -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:
@@ -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):