From 961ca05abc64cbb5dc6129b5a82dc53594d83378 Mon Sep 17 00:00:00 2001 From: ebanks Date: Sun, 11 Apr 2010 01:43:07 +0000 Subject: [PATCH] Removed outdated Sequenom rod and renamed HapMapGenotypeROD to HapMapROD. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3149 348d0f76-0448-11de-a6fe-93d51630548a --- ...{HapMapGenotypeROD.java => HapMapROD.java} | 4 +- .../sting/gatk/refdata/SequenomROD.java | 139 ------------------ .../gatk/refdata/VariantContextAdaptors.java | 4 +- .../tracks/builders/RODTrackBuilder.java | 3 +- .../sting/gatk/walkers/VariantsToVCF.java | 4 +- .../walkers/VariantsToVCFIntegrationTest.java | 2 +- 6 files changed, 8 insertions(+), 148 deletions(-) rename java/src/org/broadinstitute/sting/gatk/refdata/{HapMapGenotypeROD.java => HapMapROD.java} (90%) delete mode 100755 java/src/org/broadinstitute/sting/gatk/refdata/SequenomROD.java diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/HapMapGenotypeROD.java b/java/src/org/broadinstitute/sting/gatk/refdata/HapMapROD.java similarity index 90% rename from java/src/org/broadinstitute/sting/gatk/refdata/HapMapGenotypeROD.java rename to java/src/org/broadinstitute/sting/gatk/refdata/HapMapROD.java index 7ba9fdb64..08570a86e 100755 --- a/java/src/org/broadinstitute/sting/gatk/refdata/HapMapGenotypeROD.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/HapMapROD.java @@ -5,9 +5,9 @@ import java.util.*; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; -public class HapMapGenotypeROD extends TabularROD +public class HapMapROD extends TabularROD { - public HapMapGenotypeROD(final String name) { + public HapMapROD(final String name) { super(name); } diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/SequenomROD.java b/java/src/org/broadinstitute/sting/gatk/refdata/SequenomROD.java deleted file mode 100755 index cd9216990..000000000 --- a/java/src/org/broadinstitute/sting/gatk/refdata/SequenomROD.java +++ /dev/null @@ -1,139 +0,0 @@ -package org.broadinstitute.sting.gatk.refdata; - -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.StingException; -import org.broadinstitute.sting.utils.genotype.Variation; - -import java.util.ArrayList; -import java.util.Arrays; -import java.util.List; - -public class SequenomROD extends TabularROD implements Variation { - - public SequenomROD(String name) { - super(name); - } - - public GenomeLoc getLocation() { - long pos = Long.parseLong(this.get("1")); - return GenomeLocParser.createGenomeLoc(this.get("0"), pos); - } - - /** - * get the reference base(s) at this position - * - * @return the reference base or bases, as a string - */ - @Override - public String getReference() { - return ""; - } - - public List getFWDAlleles() { - return Arrays.asList(this.get("2")); - } - - public String getAltBasesFWD() { return getFWDAlleles().get(0); } - - /** - * get the frequency of this variant, if we're a variant. If we're reference this method - * should return 0. - * - * @return double with the stored frequency - */ - @Override - public double getNonRefAlleleFrequency() { - return 0.0; - } - - /** - * A convenience method, for switching over the variation type - * - * @return the VARIANT_TYPE of the current variant - */ - @Override - public VARIANT_TYPE getType() { - return VARIANT_TYPE.SNP; - } - - public boolean isSNP() { return true; } - public boolean isReference() { return false; } - public boolean isInsertion() { return false; } - public boolean isDeletion() { return false; } - public boolean isIndel() { return false; } - - /** - * gets the alternate base is the case of a SNP. Throws an IllegalStateException if we're not a SNP - * of - * - * @return a char, representing the alternate base - */ - @Override - public char getAlternativeBaseForSNP() { - return getAltBasesFWD().charAt(0); - } - - /** - * gets the reference base is the case of a SNP. Throws an IllegalStateException if we're not a SNP - * - * @return a char, representing the alternate base - */ - @Override - public char getReferenceForSNP() { - return 'N'; - } - - public boolean isBiallelic() { return true; } - - /** - * get the -1 * (log 10 of the error value) - * - * @return the postive number space log based error estimate - */ - @Override - public double getNegLog10PError() { - return 0.0; - } - - /** - * gets the alternate alleles. This method should return all the alleles present at the location, - * NOT including the reference base. This is returned as a string list with no guarantee ordering - * of alleles (i.e. the first alternate allele is not always going to be the allele with the greatest - * frequency). - * - * @return an alternate allele list - */ - @Override - public List getAlternateAlleleList() { - List ret = new ArrayList(); - for (char c: getAltBasesFWD().toCharArray()) - ret.add(String.valueOf(c)); - return ret; - } - - /** - * gets the alleles. This method should return all the alleles present at the location, - * including the reference base. The first allele should always be the reference allele, followed - * by an unordered list of alternate alleles. - * - * @return an alternate allele list - */ - @Override - public List getAlleleList() { - throw new StingException("SequenomRod doesn't know of the reference, and can't generate allele lists"); - } - - public boolean isHom() { return false; } - public boolean isHet() { return false; } - public double getHeterozygosity() { return 0.0; } - public double getMAF() { return 0.0; } - public int getPloidy() { return 2; } - public int length() { return 1; } - - public String toString() { - StringBuffer sb = new StringBuffer(); - sb.append(getLocation().getContig() + "\t" + getLocation().getStart() + "\t" + getFWDAlleles().get(0)); - return sb.toString(); - } - } diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java b/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java index e57e281da..40e35b956 100755 --- a/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java @@ -43,7 +43,7 @@ public class VariantContextAdaptors { adaptors.put(RodVCF.class, new RodVCFAdaptor()); adaptors.put(VCFRecord.class, new VCFRecordAdaptor()); adaptors.put(PlinkRod.class, new PlinkRodAdaptor()); - adaptors.put(HapMapGenotypeROD.class, new HapMapAdaptor()); + adaptors.put(HapMapROD.class, new HapMapAdaptor()); adaptors.put(RodGLF.class, new GLFAdaptor()); adaptors.put(RodGeliText.class, new GeliAdaptor()); } @@ -604,7 +604,7 @@ public class VariantContextAdaptors { * @return a VariantContext object */ VariantContext convert(String name, Object input, Allele refAllele) { - HapMapGenotypeROD hapmap = (HapMapGenotypeROD)input; + HapMapROD hapmap = (HapMapROD)input; // add the reference allele HashSet alleles = new HashSet(); diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RODTrackBuilder.java b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RODTrackBuilder.java index 680f37178..4534cf6d6 100644 --- a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RODTrackBuilder.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RODTrackBuilder.java @@ -63,11 +63,10 @@ public class RODTrackBuilder implements RMDTrackBuilder { Types.put("Table", TabularROD.class); Types.put("PooledEM", PooledEMSNPROD.class); Types.put("CleanedOutSNP", CleanedOutSNPROD.class); - Types.put("Sequenom", SequenomROD.class); Types.put("SangerSNP", SangerSNPROD.class); Types.put("SimpleIndel", SimpleIndelROD.class); Types.put("PointIndel", PointIndelROD.class); - Types.put("HapMapGenotype", HapMapGenotypeROD.class); + Types.put("HapMap", HapMapROD.class); Types.put("Intervals", IntervalRod.class); Types.put("Variants", RodGeliText.class); Types.put("GLF", RodGLF.class); diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java b/java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java index 11703d088..68aff5cd7 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java @@ -70,8 +70,8 @@ public class VariantsToVCF extends RodWalker { Object rod = rods.get(0); if ( rod instanceof RodVCF ) samples.addAll(Arrays.asList(((RodVCF)rod).getSampleNames())); - else if ( rod instanceof HapMapGenotypeROD ) - samples.addAll(Arrays.asList(((HapMapGenotypeROD)rod).getSampleIDs())); + else if ( rod instanceof HapMapROD ) + samples.addAll(Arrays.asList(((HapMapROD)rod).getSampleIDs())); else samples.addAll(Arrays.asList(rec.getSampleNames())); } diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/VariantsToVCFIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/VariantsToVCFIntegrationTest.java index e2f578290..73e66051d 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/VariantsToVCFIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/VariantsToVCFIntegrationTest.java @@ -58,7 +58,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-R " + oneKGLocation + "reference/human_b36_both.fasta" + - " -B variant,HapMapGenotype," + validationDataLocation + "rawHapMap.yri.chr1.txt" + + " -B variant,HapMap," + validationDataLocation + "rawHapMap.yri.chr1.txt" + " -T VariantsToVCF" + " -L 1:1-1,000,000" + " -o %s",