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Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Menachem Fromer 2011-10-18 14:49:00 -04:00
parent e5fc828546 f77f2eeb7d
commit 2125c4f38f
2 changed files with 4 additions and 2 deletions
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3
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
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@ -134,7 +134,7 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
/**
* By default, this tool throws a UserException when it encounters a field without a value in some record. This
* is generally useful when you mistype -F CHROM, so that you get a friendly warning about CHRMO not being
* is generally useful when you mistype -F CHROM, so that you get a friendly warning about CHROM not being
* found before the tool runs through 40M 1000G records. However, in some cases you genuinely want to allow such
* fields (e.g., AC not being calculated for filtered records, if included). When provided, this argument
* will cause VariantsToTable to write out NA values for missing fields instead of throwing an error.
@ -313,6 +313,7 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
getters.put("FILTER", new Getter() { public String get(VariantContext vc) {
return vc.isNotFiltered() ? "PASS" : Utils.join(",", vc.getFilters()); }
});
getters.put("ID", new Getter() { public String get(VariantContext vc) { return vc.hasID() ? vc.getID() : "."; } });
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-VAR", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getHomVarCount()); } });

3
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
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@ -381,7 +381,8 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
}
}
attributes.put(VariantContext.ID_KEY, id);
if ( ! id.equals(VCFConstants.EMPTY_ID_FIELD) )
attributes.put(VariantContext.ID_KEY, id);
return attributes;
}