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No handles (I believe) reference only VCs correctly 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3871 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2010-07-23 23:09:23 +00:00
parent e21376219d
commit b0b37c3476
1 changed files with 6 additions and 7 deletions
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13
java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
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@ -206,8 +206,6 @@ public static VariantContext simpleMerge(Collection<VariantContext> unsortedVCs,
if ( genotypeMergeOptions == GenotypeMergeType.REQUIRE_UNIQUE )
verifyUniqueSampleNames(unsortedVCs);
List<VariantContext> prepaddedVCs = sortVariantContextsByPriority(unsortedVCs, priorityListOfVCs, genotypeMergeOptions);
// Make sure all variant contexts are padded with reference base in case of indels if necessary
List<VariantContext> VCs = new ArrayList<VariantContext>();
@ -231,8 +229,8 @@ public static VariantContext simpleMerge(Collection<VariantContext> unsortedVCs,
String rsID = null;
int depth = 0;
// filtering values
int nFiltered = 0;
// counting the number of filtered and varint VCs
int nFiltered = 0, nVariant = 0;
Allele refAllele = determineReferenceAllele(VCs);
boolean remapped = false;
@ -247,6 +245,7 @@ public static VariantContext simpleMerge(Collection<VariantContext> unsortedVCs,
loc = vc.getLocation(); // get the longest location
nFiltered += vc.isFiltered() ? 1 : 0;
nVariant += vc.isVariant() ? 1 : 0;
AlleleMapper alleleMapping = resolveIncompatibleAlleles(refAllele, vc, alleles);
remapped = remapped || alleleMapping.needsRemapping();
@ -259,7 +258,6 @@ public static VariantContext simpleMerge(Collection<VariantContext> unsortedVCs,
filters.addAll(vc.getFilters());
//
// add attributes
//
@ -299,14 +297,15 @@ public static VariantContext simpleMerge(Collection<VariantContext> unsortedVCs,
// we care about where the call came from
if ( annotateOrigin ) {
String setValue;
if ( nFiltered == 0 && VCs.size() == priorityListOfVCs.size() ) // nothing was unfiltered
if ( nFiltered == 0 && nVariant == priorityListOfVCs.size() ) // nothing was unfiltered
setValue = "Intersection";
else if ( nFiltered == VCs.size() ) // everything was filtered out
setValue = "FilteredInAll";
else { // we are filtered in some subset
List<String> s = new ArrayList<String>();
for ( VariantContext vc : VCs )
s.add( vc.isFiltered() ? "filterIn" + vc.getName() : vc.getName() );
if ( vc.isVariant() )
s.add( vc.isFiltered() ? "filterIn" + vc.getName() : vc.getName() );
setValue = Utils.join("-", s);
}