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Use a sorting VCF writer because records can flip positions during left-alignment 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4583 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-10-27 06:33:03 +00:00
parent 708e973911
commit e112df20df
1 changed files with 8 additions and 3 deletions
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11
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
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@ -31,6 +31,7 @@ import net.sf.samtools.CigarOperator;
import org.broad.tribble.util.variantcontext.Allele;
import org.broad.tribble.util.variantcontext.Genotype;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broad.tribble.vcf.SortingVCFWriter;
import org.broad.tribble.vcf.VCFHeader;
import org.broad.tribble.vcf.VCFHeaderLine;
import org.broad.tribble.vcf.VCFWriter;
@ -56,14 +57,18 @@ import java.util.*;
public class LeftAlignVariants extends RodWalker<Integer, Integer> {
@Output(doc="File to which variants should be written",required=true)
protected VCFWriter writer = null;
protected VCFWriter baseWriter = null;
private SortingVCFWriter writer;
public void initialize() {
Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList("variant"));
Map<String, VCFHeader> vcfHeaders = VCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList("variant"));
Set<VCFHeaderLine> headerLines = vcfHeaders.get("variant").getMetaData();
writer.writeHeader(new VCFHeader(headerLines, samples));
baseWriter.writeHeader(new VCFHeader(headerLines, samples));
writer = new SortingVCFWriter(baseWriter, 200);
}
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
@ -115,7 +120,7 @@ public class LeftAlignVariants extends RodWalker<Integer, Integer> {
Cigar newCigar = AlignmentUtils.leftAlignIndel(originalCigar, refSeq, originalIndel, 0, 0);
// update if necessary and write
if ( !newCigar.equals(originalCigar) ) {
if ( !newCigar.equals(originalCigar) && newCigar.numCigarElements() > 1 ) {
int difference = originalIndex - newCigar.getCigarElement(0).getLength();
GenomeLoc newLoc = GenomeLocParser.createPotentiallyInvalidGenomeLoc(vc.getChr(), vc.getStart()-difference, vc.getEnd()-difference);
//System.out.println("Moving record from " + vc.getChr()+":"+vc.getStart() + " to " + newLoc);