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Fixed an issue where asking for the alternate alleles at hom-ref sites would result in an array out-of-bounds exception. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3292 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2010-05-03 18:46:33 +00:00
parent a462b5e1e7
commit 510b3efcc2
1 changed files with 6 additions and 4 deletions
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10
java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VCFSubsetWalker.java
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@ -147,13 +147,15 @@ public class VCFSubsetWalker extends RodWalker<ArrayList<VCFRecord>, VCFWriter>
VCFRecord subset = subsetRecord(record);
boolean isVariant = false;
for ( VCFGenotypeEncoding ge : subset.getVCFGenotypeRecords().get(0).getAlleles() ) {
if (!record.getReference().equals(ge.getBases())) {
isVariant = true;
if (subset.getVCFGenotypeRecords().size() > 0) {
for ( VCFGenotypeEncoding ge : subset.getVCFGenotypeRecords().get(0).getAlleles() ) {
if (!record.getReference().equals(ge.getBases())) {
isVariant = true;
}
}
}
//if (isVariant && !subset.isFiltered()) {
if ((isVariant || INCLUDE_NON_VARIANTS) && (!subset.isFiltered() || INCLUDE_FILTERED)) {
if (vwriter != null) {
vwriter.addRecord(subset);