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Fix for homopolymer bug: ref was lowercase, alt allele was uppercase, so alt != ref. Yuck. 

This is a temporary fix - pushed more elegant solution over to Matt.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2360 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-12-15 19:02:23 +00:00
parent a810586418
commit 9b0bdbbf29
1 changed files with 2 additions and 2 deletions
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4
java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
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@ -39,14 +39,14 @@ public class HomopolymerRun extends StandardVariantAnnotation {
int leftRun = 0;
for ( int i = refBasePos - 1; i >= 0; i--) {
if ( bases[i] != altAllele )
if ( Character.toUpperCase(bases[i]) != altAllele )
break;
leftRun++;
}
int rightRun = 0;
for ( int i = refBasePos + 1; i < bases.length; i++) {
if ( bases[i] != altAllele )
if ( Character.toUpperCase(bases[i]) != altAllele )
break;
rightRun++;
}