From c6081f23e5a48414419fbdb42be3870535d74e9c Mon Sep 17 00:00:00 2001 From: Christian Otto Date: Fri, 23 Aug 2019 10:59:20 +0200 Subject: [PATCH] Attempt to fix a part of #347 that leads to duplicate lines in the output --- umi_tools/sam_methods.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/umi_tools/sam_methods.py b/umi_tools/sam_methods.py index 724e1f96..889f7a8d 100644 --- a/umi_tools/sam_methods.py +++ b/umi_tools/sam_methods.py @@ -623,7 +623,7 @@ 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