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Looking over the daily error log email made me realize that there were 2 implementations of vc.modifyLocation() - the correct one in VC that didn't require lazy loading the genotype data and the bad one in VCUtils that did. Removing the implementation in VCUtils and updating the code accordingly. Also, removing createPotentiallyInvalidGenomeLoc() since no one uses it anymore. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4736 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-11-26 18:40:34 +00:00
parent 35b90d2295
commit e3e6d176df
5 changed files with 4 additions and 26 deletions
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4
java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
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@ -620,10 +620,6 @@ public class VariantContextUtils {
return uniqify ? sampleName + "." + trackName : sampleName;
}
public static VariantContext modifyLocation(VariantContext vc, GenomeLoc loc) {
return new VariantContext(vc.getSource(), loc.getContig(), loc.getStart(), loc.getStop(), vc.getAlleles(), vc.getGenotypes(), vc.getNegLog10PError(), vc.filtersWereApplied() ? vc.getFilters() : null, vc.getAttributes());
}
/**
* Returns a context identical to this with the REF and ALT alleles reverse complemented.
*

7
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
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@ -38,10 +38,8 @@ import org.broad.tribble.vcf.VCFWriter;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.sam.AlignmentUtils;
import org.broadinstitute.sting.utils.vcf.VCFUtils;
@ -136,9 +134,8 @@ public class LeftAlignVariants extends RodWalker<Integer, Integer> {
// update if necessary and write
if ( !newCigar.equals(originalCigar) && newCigar.numCigarElements() > 1 ) {
int difference = originalIndex - newCigar.getCigarElement(0).getLength();
GenomeLoc newLoc = getToolkit().getGenomeLocParser().createPotentiallyInvalidGenomeLoc(vc.getChr(), vc.getStart()-difference, vc.getEnd()-difference);
//System.out.println("Moving record from " + vc.getChr()+":"+vc.getStart() + " to " + newLoc);
VariantContext newVC = VariantContextUtils.modifyLocation(vc, newLoc);
VariantContext newVC = VariantContext.modifyLocation(vc, vc.getChr(), vc.getStart()-difference, vc.getEnd()-difference);
//System.out.println("Moving record from " + vc.getChr()+":"+vc.getStart() + " to " + vc.getChr()+":"+(vc.getStart()-difference));
int indelIndex = originalIndex-difference;
byte[] newBases = new byte[indelLength];

4
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
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@ -28,9 +28,7 @@ import org.broad.tribble.util.variantcontext.VariantContext;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.utils.vcf.VCFUtils;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@ -96,7 +94,7 @@ public class LiftoverVariants extends RodWalker<Integer, Integer> {
vc = VariantContextUtils.reverseComplement(vc);
}
vc = VariantContextUtils.modifyLocation(vc, getToolkit().getGenomeLocParser().createPotentiallyInvalidGenomeLoc(toInterval.getSequence(), toInterval.getStart(), toInterval.getStart() + length));
vc = VariantContext.modifyLocation(vc, toInterval.getSequence(), toInterval.getStart(), toInterval.getStart() + length);
VariantContext newVC = VariantContext.createVariantContextWithPaddedAlleles(vc, ref.getBase(), false);
if ( originalVC.isSNP() && VariantContextUtils.getSNPSubstitutionType(originalVC) != VariantContextUtils.getSNPSubstitutionType(newVC) ) {

13
java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
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@ -366,19 +366,6 @@ public class GenomeLocParser {
return contigInfo.getSequence(contigIndex).getSequenceName();
}
/**
* create a genome loc, given the contig name, start, and stop
*
* @param contig the contig name
* @param start the starting position
* @param stop the stop position
*
* @return a new genome loc - but don't exception out if it is invalid
*/
public GenomeLoc createPotentiallyInvalidGenomeLoc(String contig, final int start, final int stop) {
return new GenomeLoc(contig, getContigIndex(contig,false), start, stop);
}
/**
* create a genome loc, given the contig name, start, and stop
*

2
java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java
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@ -40,7 +40,7 @@ public class LiftoverVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T LiftoverVariants -o %s -R " + b36KGReference + " -B:variant,vcf " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.noheader.vcf -chain " + validationDataLocation + "b36ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict",
1,
Arrays.asList("1637877892a019061e74eb3d9a9d100f"));
Arrays.asList("cc1b1ccb800b16abce2d177c181ede56"));
executeTest("test b36 to hg19", spec);
}