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changeset 3:aa76c8dd97e6

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Reference skips have a base quality score
author Jim Johnson <jj@umn.edu>
date Tue, 19 Mar 2013 12:49:45 -0500
parents d6de2d1f4af9
children fafa105e5f58
files pileup_to_vcf.py
diffstat 1 files changed, 1 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- a/pileup_to_vcf.py	Sun Mar 03 20:38:43 2013 -0600
+++ b/pileup_to_vcf.py	Tue Mar 19 12:49:45 2013 -0500
@@ -158,6 +158,7 @@
         if debug: print >> sys.stderr, "%3d\t%s\t%3d\t%s %3d" % (bi,base,qi,quals[qi],ord(quals[qi]) - 33)
         bi += 1
         if base in '<>' :	#reference skip (between paired reads)
+          qi += 1
           pass;
         elif base in '.,' : # match reference on forward/reverse strand
           mc += 1