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Added Type.MNP to allowed variant context types; this does not break the tests (yet) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3808 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2010-07-16 15:50:25 +00:00
parent 2bdb011865
commit 6aedede7f3
1 changed files with 2 additions and 1 deletions
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3
java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java
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@ -58,7 +58,8 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
private Set<String> allowedGenotypeFormatStrings = new HashSet<String>();
// Don't allow mixed types for now
private EnumSet<VariantContext.Type> ALLOWED_VARIANT_CONTEXT_TYPES = EnumSet.of(VariantContext.Type.SNP, VariantContext.Type.NO_VARIATION, VariantContext.Type.INDEL);
private EnumSet<VariantContext.Type> ALLOWED_VARIANT_CONTEXT_TYPES = EnumSet.of(VariantContext.Type.SNP,
VariantContext.Type.NO_VARIATION, VariantContext.Type.INDEL, VariantContext.Type.MNP);
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if ( tracker == null || !BaseUtils.isRegularBase(ref.getBase()) )