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Cleanup: Use Tribble's version of createVariantContextWithPaddedAlleles (no real functional difference) to avoid duplicated code. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4315 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
delangel 2010-09-20 19:53:30 +00:00
parent a10cfe213b
commit 205fc0b636
1 changed files with 1 additions and 72 deletions
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73
java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
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@ -293,9 +293,8 @@ public class VariantContextUtils {
for (VariantContext vc : prepaddedVCs) {
// also a reasonable place to remove filtered calls, if needed
if ( ! filteredAreUncalled || vc.isNotFiltered() )
VCs.add(createVariantContextWithPaddedAlleles(vc,inputRefBase));
VCs.add(VariantContext.createVariantContextWithPaddedAlleles(vc,inputRefBase,false));
}
if ( VCs.size() == 0 ) // everything is filtered out and we're filteredareUncalled
return null;
@ -564,76 +563,6 @@ public class VariantContextUtils {
}
public static VariantContext createVariantContextWithPaddedAlleles(VariantContext inputVC, byte inputRefBase) {
Allele refAllele = inputVC.getReference();
// see if we need to pad common reference base from all alleles
boolean padVC;
// We need to pad a VC with a common base if the reference allele length is less than the vc location span.
long locLength = getLocation(inputVC).size();
if (refAllele.length() == locLength)
padVC = false;
else if (refAllele.length() == locLength-1)
padVC = true;
else throw new ReviewedStingException("Badly formed variant context, reference length must be at most one base shorter than location size");
// nothing to do if we don't need to pad bases
if (padVC) {
Byte refByte;
Map<String,Object> attributes = inputVC.getAttributes();
if (BaseUtils.isRegularBase(inputRefBase))
refByte = inputRefBase;
else if (attributes.containsKey(VariantContext.REFERENCE_BASE_FOR_INDEL_KEY))
refByte = (Byte)attributes.get(VariantContext.REFERENCE_BASE_FOR_INDEL_KEY);
else
throw new ReviewedStingException("Error when trying to pad Variant Context: either input reference base must be a regular base, or input VC must contain reference base key");
List<Allele> alleles = new ArrayList<Allele>();
Map<String, Genotype> genotypes = new TreeMap<String, Genotype>();
Map<String, Genotype> inputGenotypes = inputVC.getGenotypes();
for (Allele a : inputVC.getAlleles()) {
// get bases for current allele and create a new one with trimmed bases
String newBases = new String(new byte[]{refByte}) + a.getBaseString();
alleles.add(Allele.create(newBases,a.isReference()));
}
// now we can recreate new genotypes with trimmed alleles
for (String sample : inputVC.getSampleNames()) {
Genotype g = inputGenotypes.get(sample);
List<Allele> inAlleles = g.getAlleles();
List<Allele> newGenotypeAlleles = new ArrayList<Allele>();
for (Allele a : inAlleles) {
if (a.isCalled()) {
String newBases = new String(new byte[]{refByte}) + a.getBaseString();
newGenotypeAlleles.add(Allele.create(newBases,a.isReference()));
}
else {
// add no-call allele
newGenotypeAlleles.add(Allele.NO_CALL);
}
}
genotypes.put(sample, new Genotype(sample, newGenotypeAlleles, g.getNegLog10PError(),
g.getFilters(),g.getAttributes(),g.genotypesArePhased()));
}
return new VariantContext(inputVC.getName(), inputVC.getChr(), inputVC.getStart(), inputVC.getEnd(), alleles, genotypes, inputVC.getNegLog10PError(),
inputVC.getFilters(), attributes);
}
else
return inputVC;
}
static class CompareByPriority implements Comparator<VariantContext>, Serializable {
List<String> priorityListOfVCs;