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Fix for incorrect output of dedup with --paired (#347) #363

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Fix for incorrect output of dedup with --paired (#347) #363

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Fix for incorrect output of dedup with --paired (#347)
christianbioinf Jul 5, 2019
78f457b
Improvement of consistency in selection of read2 alignments for outpu…
christianbioinf Jul 8, 2019
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8 changes: 4 additions & 4 deletions umi_tools/sam_methods.py
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Original file line number Diff line number Diff line change
Expand Up @@ -589,7 +589,7 @@ def write(self, read, unique_id=None, umi=None, unmapped=False):
self.write_mates()
self.chrom = read.reference_name

key = read.query_name, read.next_reference_name, read.next_reference_start
key = read.query_name, read.next_reference_name, read.next_reference_start, read.reference_name, read.reference_start
self.read1s.add(key)

self.outfile.write(read)
Expand All @@ -605,7 +605,7 @@ def write_mates(self):
if any((read.is_unmapped, read.mate_is_unmapped, read.is_read1)):
continue

key = read.query_name, read.reference_name, read.reference_start
key = read.query_name, read.reference_name, read.reference_start, read.next_reference_name, read.next_reference_start
if key in self.read1s:
self.outfile.write(read)
self.read1s.remove(key)
Expand All @@ -623,10 +623,10 @@ def close(self):
found = 0
for read in self.infile.fetch(until_eof=True, multiple_iterators=True):

if read.is_unmapped:
if any((read.is_unmapped, read.mate_is_unmapped, read.is_read1)):
continue

key = read.query_name, read.reference_name, read.reference_start
key = read.query_name, read.reference_name, read.reference_start, read.next_reference_name, read.next_reference_start
if key in self.read1s:
self.outfile.write(read)
self.read1s.remove(key)
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