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Prevent array bounds errors 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1435 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-08-18 16:54:31 +00:00
parent 26a6f816c9
commit 82e2b7017e
1 changed files with 1 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelFilterWalker.java
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@ -77,7 +77,7 @@ public class IndelFilterWalker extends RefWalker<Integer, Integer> {
leftRun++;
}
indelBase = indel.isDeletion() ? bases[refBasePos+indel.length()] : indel.getAltBasesFWD().charAt(indel.getAltBasesFWD().length()-1);
indelBase = indel.isDeletion() ? bases[Math.min(refBasePos+indel.length(),bases.length-1)] : indel.getAltBasesFWD().charAt(indel.getAltBasesFWD().length()-1);
int rightRun = 0;
for ( int i = refBasePos + (indel.isDeletion() ? 1+indel.length() : 1); i < bases.length; i++) {
if ( bases[i] != indelBase )