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Proper filtering when indels are being lifted over 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4158 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-08-29 04:48:31 +00:00
parent 2ffa98aea5
commit df76474b34
1 changed files with 15 additions and 8 deletions
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23
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
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@ -40,6 +40,7 @@ import java.util.*;
/**
* Filters a lifted-over VCF file for ref bases that have been changed.
*/
@Reference(window=@Window(start=0,stop=100))
@Requires(value={},referenceMetaData=@RMD(name="variant",type= VariantContext.class))
public class FilterLiftedVariants extends RodWalker<Integer, Integer> {
@ -56,17 +57,23 @@ public class FilterLiftedVariants extends RodWalker<Integer, Integer> {
writer.writeHeader(vcfHeader);
}
private void filterAndWrite(byte ref, VariantContext vc) {
private void filterAndWrite(byte[] ref, VariantContext vc) {
totalLocs++;
byte recordRef = vc.getReference().getBases()[0];
if ( recordRef != ref ) {
failedLocs++;
} else {
writer.add(vc, ref);
boolean failed = false;
byte[] recordRef = vc.getReference().getBases();
for (int i = 0; i < recordRef.length; i++) {
if ( recordRef[i] != ref[i + (vc.isSNP() ? 0 : 1)] ) {
failed = true;
break;
}
}
if ( failed )
failedLocs++;
else
writer.add(vc, ref[0]);
}
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
@ -75,7 +82,7 @@ public class FilterLiftedVariants extends RodWalker<Integer, Integer> {
Collection<VariantContext> VCs = tracker.getVariantContexts(ref, "variant", null, context.getLocation(), true, false);
for ( VariantContext vc : VCs )
filterAndWrite(ref.getBase(), vc);
filterAndWrite(ref.getBases(), vc);
return 0;
}