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Bug fix: merge NO_VARIATION records with those of another type. The sad part is that this WAS covered by integration tests but someone updated the MD5s without actually paying attention...

This commit is contained in:
Eric Banks 2012-03-21 12:42:13 -04:00
parent dcf2fa361d
commit 07c3bd32b3
2 changed files with 14 additions and 1 deletions
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13
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
View File

@ -243,6 +243,19 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
if (multipleAllelesMergeType == VariantContextUtils.MultipleAllelesMergeType.BY_TYPE) {
Map<VariantContext.Type, List<VariantContext>> VCsByType = VariantContextUtils.separateVariantContextsByType(vcs);
// TODO -- clean this up in a refactoring
// merge NO_VARIATION into another type of variant (based on the ordering in VariantContext.Type)
if ( VCsByType.containsKey(VariantContext.Type.NO_VARIATION) && VCsByType.size() > 1 ) {
final List<VariantContext> refs = VCsByType.remove(VariantContext.Type.NO_VARIATION);
for ( VariantContext.Type type : VariantContext.Type.values() ) {
if ( VCsByType.containsKey(type) ) {
VCsByType.get(type).addAll(refs);
break;
}
}
}
// iterate over the types so that it's deterministic
for (VariantContext.Type type : VariantContext.Type.values()) {
if (VCsByType.containsKey(type))

2
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
View File

@ -110,7 +110,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
" -priority NA19240_BGI,NA19240_ILLUMINA,NA19240_WUGSC,denovoInfo" +
" -genotypeMergeOptions UNIQUIFY -L 1"),
1,
Arrays.asList("ab72f4bfb16d3894942149173a087647"));
Arrays.asList("ee43a558fd3faeaa447acab89f0001d5"));
executeTest("threeWayWithRefs", spec);
}