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Set the priority list and don't bother combining if not needed

This commit is contained in:
Joel Thibault 2012-04-20 14:18:19 -04:00
parent f739305f43
commit a7fe847faf
1 changed files with 5 additions and 2 deletions
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7
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -665,12 +665,15 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
} }
// Copied from CombineVariants // Copied from CombineVariants
private Collection<VariantContext> combineVariants(ArrayList<VariantContext> vcs) { private Collection<VariantContext> combineVariants(Collection<VariantContext> vcs) {
if (vcs.size() < 2)
return vcs;
List<VariantContext> mergedVCs = new ArrayList<VariantContext>(); List<VariantContext> mergedVCs = new ArrayList<VariantContext>();
//defaults from CombineVariants //defaults from CombineVariants
VariantContextUtils.MultipleAllelesMergeType multipleAllelesMergeType = VariantContextUtils.MultipleAllelesMergeType.BY_TYPE; VariantContextUtils.MultipleAllelesMergeType multipleAllelesMergeType = VariantContextUtils.MultipleAllelesMergeType.BY_TYPE;
List<String> priority = null; List<String> priority = new ArrayList<String>(VCFUtils.getVCFHeadersFromRods(getToolkit()).keySet());
VariantContextUtils.FilteredRecordMergeType filteredRecordsMergeType = VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED; VariantContextUtils.FilteredRecordMergeType filteredRecordsMergeType = VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED;
VariantContextUtils.GenotypeMergeType genotypeMergeOption = VariantContextUtils.GenotypeMergeType.PRIORITIZE; VariantContextUtils.GenotypeMergeType genotypeMergeOption = VariantContextUtils.GenotypeMergeType.PRIORITIZE;
boolean printComplexMerges = false; boolean printComplexMerges = false;