{is} fix chimeric mates (#707)

* Fixes #664 - reverts to using multiple iterators in the TwoPassWriter close method, but not write mates. This still saves the time from opening many iterators everything the contig is changed, but doesn't lose chimeric reads.

Author: IanSudbery

umi_tools/sam_methods.py

@@ -625,7 +625,7 @@ def close(self):
                len(self.read1s))
 
         found = 0
-        for read in self.mate_file.fetch(until_eof=True, multiple_iterators=False):
+        for read in self.mate_file.fetch(until_eof=True, multiple_iterators=True):
 
             if any((read.is_unmapped, read.mate_is_unmapped, read.is_read1)):
                 continue