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Bugfix for not setting header in AbstractVCFCodec

This commit is contained in:
Mark DePristo 2012-05-22 16:40:01 -04:00
parent 6ca71fe3b4
commit ade1843818
2 changed files with 3 additions and 2 deletions
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3
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
View File

@ -176,7 +176,8 @@ public abstract class AbstractVCFCodec extends AsciiFeatureCodec<VariantContext>
}
}
return new VCFHeader(metaData, sampleNames);
this.header = new VCFHeader(metaData, sampleNames);
return this.header;
}
/**

2
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java
View File

@ -88,7 +88,7 @@ public class VCFCodec extends AbstractVCFCodec {
throw new TribbleException.InvalidHeader("We never saw a header line specifying VCF version");
}
headerStrings.add(line);
this.header = super.parseHeaderFromLines(headerStrings, version);
super.parseHeaderFromLines(headerStrings, version);
if ( headerForRepairs != null )
this.header = repairHeader(this.header, headerForRepairs);
return this.header;