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Combine the variants found at a location

This commit is contained in:
Joel Thibault 2012-04-20 14:04:31 -04:00
parent 020f884d5a
commit f739305f43
1 changed files with 62 additions and 1 deletions
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63
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -661,7 +661,68 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
vcs.add(builder.make());
}
return vcs;
return combineVariants(vcs);
}
// Copied from CombineVariants
private Collection<VariantContext> combineVariants(ArrayList<VariantContext> vcs) {
List<VariantContext> mergedVCs = new ArrayList<VariantContext>();
//defaults from CombineVariants
VariantContextUtils.MultipleAllelesMergeType multipleAllelesMergeType = VariantContextUtils.MultipleAllelesMergeType.BY_TYPE;
List<String> priority = null;
VariantContextUtils.FilteredRecordMergeType filteredRecordsMergeType = VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED;
VariantContextUtils.GenotypeMergeType genotypeMergeOption = VariantContextUtils.GenotypeMergeType.PRIORITIZE;
boolean printComplexMerges = false;
String SET_KEY = "set";
boolean filteredAreUncalled = false;
boolean MERGE_INFO_WITH_MAX_AC = false;
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))
mergedVCs.add(VariantContextUtils.simpleMerge(getToolkit().getGenomeLocParser(), VCsByType.get(type),
priority, filteredRecordsMergeType, genotypeMergeOption, true, printComplexMerges,
SET_KEY, filteredAreUncalled, MERGE_INFO_WITH_MAX_AC));
}
}
else if (multipleAllelesMergeType == VariantContextUtils.MultipleAllelesMergeType.MIX_TYPES) {
mergedVCs.add(VariantContextUtils.simpleMerge(getToolkit().getGenomeLocParser(), vcs,
priority, filteredRecordsMergeType, genotypeMergeOption, true, printComplexMerges,
SET_KEY, filteredAreUncalled, MERGE_INFO_WITH_MAX_AC));
}
else {
logger.warn("Ignoring all records at site");
}
List<VariantContext> recomputedVCs = new ArrayList<VariantContext>();
for ( VariantContext mergedVC : mergedVCs ) {
// only operate at the start of events
if ( mergedVC == null )
continue;
final VariantContextBuilder builder = new VariantContextBuilder(mergedVC);
// re-compute chromosome counts
VariantContextUtils.calculateChromosomeCounts(builder, false);
recomputedVCs.add(builder.make());
}
return recomputedVCs;
}
/**