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If the first base of a read is 'N', and the alignment cigar says every base matches, samtools calls shennanigans. Now I just output an A, but the real way to do this is to modify the cigar string accordingly. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@337 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-04-08 19:58:18 +00:00
parent 0e7d962eca
commit eb2f0ebd62
1 changed files with 1 additions and 1 deletions
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java/src/org/broadinstitute/sting/playground/fourbasecaller/RepairBadlyCombinedSamFile.java
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@ -50,7 +50,7 @@ public class RepairBadlyCombinedSamFile extends CommandLineProgram {
case 'C': newbase = 'G'; break; case 'C': newbase = 'G'; break;
case 'G': newbase = 'C'; break; case 'G': newbase = 'C'; break;
case 'T': newbase = 'A'; break; case 'T': newbase = 'A'; break;
default: newbase = '.'; default: newbase = 'A'; // hack. This is so downstream applications don't barf on an ambiguous base 'matching' the reference
} }
newbases[i] = newbase; newbases[i] = newbase;
newquals[i] = quals[bases.length - i - 1]; newquals[i] = quals[bases.length - i - 1];