# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1363715385 18000
# Node ID aa76c8dd97e601c0f210d10685984827cb6978d3
# Parent  d6de2d1f4af9e4141d17c79e6f4c9a1d0e397347
Reference skips have a base quality score

diff -r d6de2d1f4af9 -r aa76c8dd97e6 pileup_to_vcf.py
--- 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