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Resolving merge conflicts

This commit is contained in:
Eric Banks 2011-08-15 12:28:05 -04:00
parent ca9bb841c3 9ddbfdcb9f
commit 3d56bbf087
1 changed files with 12 additions and 11 deletions
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23
public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
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@ -66,17 +66,18 @@ public class FastaAlternateReferenceWalker extends FastaReferenceWalker {
String refBase = String.valueOf((char)ref.getBase()); String refBase = String.valueOf((char)ref.getBase());
// Check to see if we have a called snp // Check to see if we have a called snp
for ( VariantContext vc : tracker.getValues(VariantContext.class) ) { for ( VariantContext vc : tracker.getValues(variants) ) {
if ( ! vc.getSource().equals(snpmask.getName())) { if ( vc.isFiltered() )
if ( vc.isDeletion()) { continue;
deletionBasesRemaining = vc.getReference().length();
// delete the next n bases, not this one if ( vc.isDeletion()) {
return new Pair<GenomeLoc, String>(context.getLocation(), refBase); deletionBasesRemaining = vc.getReference().length();
} else if ( vc.isInsertion()) { // delete the next n bases, not this one
return new Pair<GenomeLoc, String>(context.getLocation(), refBase.concat(vc.getAlternateAllele(0).toString())); return new Pair<GenomeLoc, String>(context.getLocation(), refBase);
} else if (vc.isSNP()) { } else if ( vc.isInsertion()) {
return new Pair<GenomeLoc, String>(context.getLocation(), vc.getAlternateAllele(0).toString()); return new Pair<GenomeLoc, String>(context.getLocation(), refBase.concat(vc.getAlternateAllele(0).toString()));
} } else if (vc.isSNP()) {
return new Pair<GenomeLoc, String>(context.getLocation(), vc.getAlternateAllele(0).toString());
} }
} }