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Don't create a record if ref=N 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2018 348d0f76-0448-11de-a6fe-93d51630548a
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ebanks 2009-11-11 04:32:17 +00:00
parent 8406325247
commit 578dcc54a4
1 changed files with 1 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/VariantsToVCF.java
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@ -136,7 +136,7 @@ public class VariantsToVCF extends RefWalker<Integer, Integer> {
numSNPs++;
snpQual += av.getNegLog10PError();
} else {
} else if (BaseUtils.simpleBaseToBaseIndex(ref.getBase()) != -1) {
Map<String, String> str = new HashMap<String, String>();
List<VCFGenotypeEncoding> alleles = new ArrayList<VCFGenotypeEncoding>();
alleles.add(new VCFGenotypeEncoding(String.valueOf(ref.getBase())));