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Optional argument to put the original position into the INFO field 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4930 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-01-04 19:22:44 +00:00
parent caedfed860
commit 96729acd0d
1 changed files with 22 additions and 4 deletions
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26
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
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@ -25,6 +25,7 @@
package org.broadinstitute.sting.gatk.walkers.variantutils;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broad.tribble.vcf.*;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.utils.vcf.VCFUtils;
@ -34,8 +35,6 @@ import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
import org.broad.tribble.vcf.VCFHeader;
import org.broad.tribble.vcf.StandardVCFWriter;
import java.io.File;
import java.util.*;
@ -61,6 +60,9 @@ public class LiftoverVariants extends RodWalker<Integer, Integer> {
@Argument(fullName="newSequenceDictionary", shortName="dict", doc="Sequence .dict file for the new build", required=true)
protected File NEW_SEQ_DICT = null;
@Argument(fullName="recordOriginalLocation", shortName="recordOriginalLocation", doc="Should we record what the original location was in the INFO field?", required=false)
protected Boolean RECORD_ORIGINAL_LOCATION = false;
private LiftOver liftOver;
private long successfulIntervals = 0, failedIntervals = 0;
@ -75,7 +77,16 @@ public class LiftoverVariants extends RodWalker<Integer, Integer> {
Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList("variant"));
Map<String, VCFHeader> vcfHeaders = VCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList("variant"));
final VCFHeader vcfHeader = new VCFHeader(vcfHeaders.containsKey("variant") ? vcfHeaders.get("variant").getMetaData() : null, samples);
Set<VCFHeaderLine> metaData = new HashSet<VCFHeaderLine>();
if ( vcfHeaders.containsKey("variant") )
metaData.addAll(vcfHeaders.get("variant").getMetaData());
if ( RECORD_ORIGINAL_LOCATION ) {
metaData.add(new VCFInfoHeaderLine("OriginalChr", 1, VCFHeaderLineType.String, "Original contig name for the record"));
metaData.add(new VCFInfoHeaderLine("OriginalStart", 1, VCFHeaderLineType.Integer, "Original start position for the record"));
}
final VCFHeader vcfHeader = new VCFHeader(metaData, samples);
writer = new StandardVCFWriter(file, false);
writer.writeHeader(vcfHeader);
}
@ -95,8 +106,15 @@ public class LiftoverVariants extends RodWalker<Integer, Integer> {
}
vc = VariantContext.modifyLocation(vc, toInterval.getSequence(), toInterval.getStart(), toInterval.getStart() + length);
VariantContext newVC = VariantContext.createVariantContextWithPaddedAlleles(vc, ref.getBase(), false);
if ( RECORD_ORIGINAL_LOCATION ) {
HashMap<String, Object> attrs = new HashMap<String, Object>(vc.getAttributes());
attrs.put("OriginalChr", fromInterval.getSequence());
attrs.put("OriginalStart", fromInterval.getStart());
vc = VariantContext.modifyAttributes(vc, attrs);
}
VariantContext newVC = VariantContext.createVariantContextWithPaddedAlleles(vc, ref.getBase(), false);
if ( originalVC.isSNP() && originalVC.isBiallelic() && VariantContextUtils.getSNPSubstitutionType(originalVC) != VariantContextUtils.getSNPSubstitutionType(newVC) ) {
logger.warn(String.format("VCF at %s / %d => %s / %d is switching substitution type %s/%s to %s/%s",
originalVC.getChr(), originalVC.getStart(), newVC.getChr(), newVC.getStart(),