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Check for bad reference bases before creating simple/'empty' VCs. Updated the code in the indel GL model to be consistent and to use the existing utility in the Allele class. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5704 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-04-27 23:55:20 +00:00
parent 122d5845d3
commit ae8f3f2cde
2 changed files with 6 additions and 10 deletions
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12
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
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@ -231,23 +231,15 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
//System.out.println(new String(ref.getBases())); //System.out.println(new String(ref.getBases()));
byte[] refBases = Arrays.copyOfRange(ref.getBases(),startIdxInReference,startIdxInReference+dLen); byte[] refBases = Arrays.copyOfRange(ref.getBases(),startIdxInReference,startIdxInReference+dLen);
boolean ok = true;
for (int i=0; i < refBases.length; i++)
if (!BaseUtils.isRegularBase(refBases[i]))
ok = false;
if (ok) { if (Allele.acceptableAlleleBases(refBases)) {
refAllele = Allele.create(refBases,true); refAllele = Allele.create(refBases,true);
altAllele = Allele.create(Allele.NULL_ALLELE_STRING, false); altAllele = Allele.create(Allele.NULL_ALLELE_STRING, false);
} }
} }
else { else {
// insertion case // insertion case
boolean ok = true; if (Allele.acceptableAlleleBases(bestAltAllele)) {
for (int i=0; i < bestAltAllele.length(); i++)
if (!BaseUtils.isRegularBase(bestAltAllele.getBytes()[i]))
ok = false;
if (ok) {
refAllele = Allele.create(Allele.NULL_ALLELE_STRING, true); refAllele = Allele.create(Allele.NULL_ALLELE_STRING, true);
altAllele = Allele.create(bestAltAllele, false); altAllele = Allele.create(bestAltAllele, false);
} }

4
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
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@ -203,6 +203,10 @@ public class UnifiedGenotyperEngine {
return null; return null;
vc = new VariantContext("UG_call", vcInput.getChr(), vcInput.getStart(), vcInput.getEnd(), vcInput.getAlleles()); vc = new VariantContext("UG_call", vcInput.getChr(), vcInput.getStart(), vcInput.getEnd(), vcInput.getAlleles());
} else { } else {
// deal with bad/non-standard reference bases
if ( !Allele.acceptableAlleleBases(new byte[]{ref.getBase()}) )
return null;
Set<Allele> alleles = new HashSet<Allele>(); Set<Allele> alleles = new HashSet<Allele>();
alleles.add(Allele.create(ref.getBase(), true)); alleles.add(Allele.create(ref.getBase(), true));
vc = new VariantContext("UG_call", ref.getLocus().getContig(), ref.getLocus().getStart(), ref.getLocus().getStart(), alleles); vc = new VariantContext("UG_call", ref.getLocus().getContig(), ref.getLocus().getStart(), ref.getLocus().getStart(), alleles);