From e3e6d176df3e24de6be5a9af870775aec94bf9a1 Mon Sep 17 00:00:00 2001 From: ebanks Date: Fri, 26 Nov 2010 18:40:34 +0000 Subject: [PATCH] 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 --- .../variantcontext/VariantContextUtils.java | 4 ---- .../walkers/variantutils/LeftAlignVariants.java | 7 ++----- .../gatk/walkers/variantutils/LiftoverVariants.java | 4 +--- .../broadinstitute/sting/utils/GenomeLocParser.java | 13 ------------- .../LiftoverVariantsIntegrationTest.java | 2 +- 5 files changed, 4 insertions(+), 26 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java index e0121cb54..d755a7ecc 100755 --- a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java +++ b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java @@ -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. * diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java index 485af6261..2054c083d 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java @@ -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 { // 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]; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java index 5ece5f8fe..1749a13cf 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java @@ -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 { 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) ) { diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java b/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java index 8ea108fe1..8cc405a21 100644 --- a/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java +++ b/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java @@ -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 * diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java index 737a5910c..4f5be716a 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java @@ -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); }