Merge pull request #366 from christianbioinf/{IS}_dedup_with_paired_d…

…uplicated_lines Fix for incorrect output of dedup with --paired (#347) in case of duplicated lines
CGATOxford · Aug 23, 2019 · 6945f6a · 6945f6a
2 parents e8c2b47 + c6081f2
commit 6945f6a
Showing 1 changed file with 1 addition and 1 deletion.
diff --git 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