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Now prints out PASS when a variant is unfiltered 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4318 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2010-09-21 13:16:41 +00:00
parent 21a34daf2e
commit 8719dde59d
1 changed files with 3 additions and 1 deletions
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4
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
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@ -87,7 +87,9 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
} }
}); });
getters.put("QUAL", new Getter() { public String get(VariantContext vc) { return Double.toString(vc.getPhredScaledQual()); } }); getters.put("QUAL", new Getter() { public String get(VariantContext vc) { return Double.toString(vc.getPhredScaledQual()); } });
getters.put("FILTER", new Getter() { public String get(VariantContext vc) { return Utils.join(",", vc.getFilters()); } }); getters.put("FILTER", new Getter() { public String get(VariantContext vc) {
return vc.isNotFiltered() ? "PASS" : Utils.join(",", vc.getFilters()); }
});
getters.put("HET", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getHetCount()); } }); getters.put("HET", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getHetCount()); } });
getters.put("HOM-REF", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getHomRefCount()); } }); getters.put("HOM-REF", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getHomRefCount()); } });