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Don't list '.' as an alternate allele, dummy! 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3337 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2010-05-10 14:51:18 +00:00
parent 98718d0faa
commit b223b04331
1 changed files with 3 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VCFSubsetWalker.java
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@ -125,8 +125,10 @@ public class VCFSubsetWalker extends RodWalker<ArrayList<VCFRecord>, VCFWriter>
ArrayList<VCFGenotypeEncoding> genotypeEncodings = new ArrayList<VCFGenotypeEncoding>(); ArrayList<VCFGenotypeEncoding> genotypeEncodings = new ArrayList<VCFGenotypeEncoding>();
for (VCFGenotypeEncoding allele : genotypeEncodingSet) { for (VCFGenotypeEncoding allele : genotypeEncodingSet) {
if (!allele.getBases().equalsIgnoreCase(".")) {
genotypeEncodings.add(allele); genotypeEncodings.add(allele);
} }
}
VCFRecord subset = new VCFRecord(record.getReference(), VCFRecord subset = new VCFRecord(record.getReference(),
record.getChr(), record.getChr(),