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For Chris, to make his life easier: iterate over all VCF records passed in looking for one with an ALT allele defined instead of assuming all records have one. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4789 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-12-05 02:23:38 +00:00
parent 97c94176c0
commit bef48e7a42
1 changed files with 13 additions and 6 deletions
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19
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCallVariants.java
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@ -95,7 +95,6 @@ public class UGCallVariants extends RodWalker<VariantCallContext, Integer> {
if ( tracker == null )
return null;
List<VariantContext> VCs = new ArrayList<VariantContext>();
for ( String name : trackNames ) {
Collection<VariantContext> vc = tracker.getVariantContexts(ref, name, null, context.getLocation(), true, true);
@ -135,11 +134,19 @@ public class UGCallVariants extends RodWalker<VariantCallContext, Integer> {
if ( VCs.size() == 0 )
return null;
VariantContext vc = VCs.get(0);
Map<String, Genotype> genotypes = new HashMap<String, Genotype>(getGenotypesWithGLs(vc.getGenotypes()));
for (int i = 1; i < VCs.size(); i++)
genotypes.putAll(getGenotypesWithGLs(VCs.get(i).getGenotypes()));
return new VariantContext("VCwithGLs", vc.getChr(), vc.getStart(), vc.getEnd(), vc.getAlleles(), genotypes, VariantContext.NO_NEG_LOG_10PERROR, null, null);
VariantContext variantVC = null;
Map<String, Genotype> genotypes = new HashMap<String, Genotype>();
for ( VariantContext vc : VCs ) {
if ( variantVC == null && vc.isVariant() )
variantVC = vc;
genotypes.putAll(getGenotypesWithGLs(vc.getGenotypes()));
}
if ( variantVC == null ) {
VariantContext vc = VCs.get(0);
throw new UserException("There is no ALT allele in any of the VCF records passed in at " + vc.getChr() + ":" + vc.getStart());
}
return new VariantContext("VCwithGLs", variantVC.getChr(), variantVC.getStart(), variantVC.getEnd(), variantVC.getAlleles(), genotypes, VariantContext.NO_NEG_LOG_10PERROR, null, null);
}
private static Map<String, Genotype> getGenotypesWithGLs(Map<String, Genotype> genotypes) {