Mercurial > repos > jjohnson > pileup_to_vcf
comparison pileup_to_vcf.py @ 3:aa76c8dd97e6
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 |
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| 2:d6de2d1f4af9 | 3:aa76c8dd97e6 |
|---|---|
| 156 while bi < len(bases): | 156 while bi < len(bases): |
| 157 base = bases[bi] | 157 base = bases[bi] |
| 158 if debug: print >> sys.stderr, "%3d\t%s\t%3d\t%s %3d" % (bi,base,qi,quals[qi],ord(quals[qi]) - 33) | 158 if debug: print >> sys.stderr, "%3d\t%s\t%3d\t%s %3d" % (bi,base,qi,quals[qi],ord(quals[qi]) - 33) |
| 159 bi += 1 | 159 bi += 1 |
| 160 if base in '<>' : #reference skip (between paired reads) | 160 if base in '<>' : #reference skip (between paired reads) |
| 161 qi += 1 | |
| 161 pass; | 162 pass; |
| 162 elif base in '.,' : # match reference on forward/reverse strand | 163 elif base in '.,' : # match reference on forward/reverse strand |
| 163 mc += 1 | 164 mc += 1 |
| 164 adp += 1 | 165 adp += 1 |
| 165 qual = ord(quals[qi]) -33 | 166 qual = ord(quals[qi]) -33 |