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Check filtered status before applying to alt reference

This commit is contained in:
Eric Banks 2011-08-15 12:25:23 -04:00
parent 8325cb8c26
commit 9ddbfdcb9f
1 changed files with 2 additions and 0 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
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@ -61,6 +61,8 @@ public class FastaAlternateReferenceWalker extends FastaReferenceWalker {
// Check to see if we have a called snp // Check to see if we have a called snp
for ( VariantContext vc : vcs ) { for ( VariantContext vc : vcs ) {
if ( vc.isFiltered() )
continue;
if ( !vc.getSource().startsWith("snpmask") ) { if ( !vc.getSource().startsWith("snpmask") ) {
if ( vc.isDeletion()) { if ( vc.isDeletion()) {
deletionBasesRemaining = vc.getReference().length(); deletionBasesRemaining = vc.getReference().length();