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Bug fix for Tim: all point events must be treated equally 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4629 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-11-05 03:42:51 +00:00
parent 0e40321a52
commit c9dbd8f80a
2 changed files with 3 additions and 3 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
View File

@ -66,7 +66,7 @@ public class FilterLiftedVariants extends RodWalker<Integer, Integer> {
boolean failed = false;
byte[] recordRef = vc.getReference().getBases();
for (int i = 0; i < recordRef.length && i < MAX_VARIANT_SIZE; i++) {
if ( recordRef[i] != ref[i + (vc.isSNP() ? 0 : 1)] ) {
if ( recordRef[i] != ref[i + (vc.isPointEvent() ? 0 : 1)] ) {
failed = true;
break;
}

4
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
View File

@ -92,14 +92,14 @@ public class LiftoverVariants extends RodWalker<Integer, Integer> {
if ( toInterval != null ) {
// check whether the strand flips, and if so reverse complement everything
// TODO -- make this work for indels (difficult because the 'previous base' context needed will be changing based on indel type/size)
if ( fromInterval.isPositiveStrand() != toInterval.isPositiveStrand() && (vc.isSNP() || !vc.isVariant()) ) {
if ( fromInterval.isPositiveStrand() != toInterval.isPositiveStrand() && vc.isPointEvent() ) {
vc = VariantContextUtils.reverseComplement(vc);
}
vc = VariantContextUtils.modifyLocation(vc, GenomeLocParser.createPotentiallyInvalidGenomeLoc(toInterval.getSequence(), toInterval.getStart(), toInterval.getStart() + length));
VariantContext newVC = VariantContext.createVariantContextWithPaddedAlleles(vc, ref.getBase(), false);
if ( originalVC.isVariant() && VariantContextUtils.getSNPSubstitutionType(originalVC) != VariantContextUtils.getSNPSubstitutionType(newVC) ) {
if ( originalVC.isSNP() && VariantContextUtils.getSNPSubstitutionType(originalVC) != VariantContextUtils.getSNPSubstitutionType(newVC) ) {
logger.warn(String.format("VCF at %s / %d => %s / %d is switching substitution type %s/%s to %s/%s",
originalVC.getChr(), originalVC.getStart(), newVC.getChr(), newVC.getStart(),
originalVC.getReference(), originalVC.getAlternateAllele(0), newVC.getReference(), newVC.getAlternateAllele(0)));