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Adding headers to diffable reading for VCFs

This commit is contained in:
Eric Banks 2011-07-14 13:55:35 -04:00
parent 57a90173f3
commit ed6beae1f3
1 changed files with 6 additions and 6 deletions
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12
public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
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@ -26,16 +26,12 @@ package org.broadinstitute.sting.gatk.walkers.diffengine;
import org.broad.tribble.readers.AsciiLineReader;
import org.broad.tribble.readers.LineReader;
import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.io.*;
import java.util.Arrays;
import java.util.Map;
import java.util.zip.GZIPInputStream;
/**
@ -58,7 +54,11 @@ public class VCFDiffableReader implements DiffableReader {
VCFCodec vcfCodec = new VCFCodec();
// must be read as state is stored in reader itself
vcfCodec.readHeader(lineReader);
VCFHeader header = (VCFHeader)vcfCodec.readHeader(lineReader);
for ( VCFHeaderLine headerLine : header.getMetaData() ) {
final String key = (headerLine instanceof VCFNamedHeaderLine ? headerLine.getKey() + "." + ((VCFNamedHeaderLine) headerLine).getName() : headerLine.getKey());
root.add(key, headerLine.toString());
}
String line = lineReader.readLine();
int count = 0;