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fix for the eval tests, and a change to the backedbygenotypes interface, more changes to come 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1661 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-09-18 22:25:16 +00:00
parent 4318f75910
commit b6d7d6acc6
6 changed files with 70 additions and 65 deletions
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10
java/src/org/broadinstitute/sting/gatk/refdata/RodGeliText.java
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@ -266,7 +266,6 @@ public class RodGeliText extends BasicReferenceOrderedDatum implements Variation
public List<String> getGenotype() throws IllegalStateException {
return Arrays.asList(getBestGenotype());
//throw new IllegalStateException("huh?");
}
public int getPloidy() throws IllegalStateException {
@ -348,14 +347,13 @@ public class RodGeliText extends BasicReferenceOrderedDatum implements Variation
/**
* get the likelihoods
* get the genotype
*
* @return an array in lexigraphical order of the likelihoods
* @return a map in lexigraphical order of the genotypes
*/
@Override
public Genotype getGenotype(DiploidGenotype x) {
if (x.toString() != this.getAltBasesFWD()) throw new IllegalStateException("We don't contain genotype " + x);
return new BasicGenotype(getLocation(), x.toString(), refBase, lodBtnb);
public Genotype getCallexGenotype() {
return new BasicGenotype(getLocation(), this.getAltBasesFWD(), refBase, lodBtnb);
}
/**

21
java/src/org/broadinstitute/sting/gatk/refdata/RodGenotypeChipAsGFF.java
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@ -259,6 +259,16 @@ public class RodGenotypeChipAsGFF extends BasicReferenceOrderedDatum implements
public boolean isBiallelic() { return true; }
public int length() { return 1; }
/**
* get the genotype
*
* @return a map in lexigraphical order of the genotypes
*/
@Override
public Genotype getCallexGenotype() {
return new BasicGenotype(this.getLocation(),this.feature,this.getRefSnpFWD(),this.getConsensusConfidence());
}
/**
* get the likelihoods
*
@ -270,17 +280,6 @@ public class RodGenotypeChipAsGFF extends BasicReferenceOrderedDatum implements
ret.add(new BasicGenotype(this.getLocation(),this.feature,this.getRefSnpFWD(),this.getConsensusConfidence()));
return ret;
}
/**
* get the likelihoods
*
* @return an array in lexigraphical order of the likelihoods
*/
@Override
public Genotype getGenotype(DiploidGenotype x) {
if (!x.toString().equals(this.getAltBasesFWD())) throw new IllegalStateException("Unable to retrieve genotype");
return new BasicGenotype(this.getLocation(),this.feature,this.getRefSnpFWD(),this.getConsensusConfidence());
}
/**
* do we have the specified genotype? not all backedByGenotypes

37
java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java
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@ -249,6 +249,16 @@ public class RodVCF extends BasicReferenceOrderedDatum implements Variation, Var
return mCurrentRecord.getReferenceBase();
}
/**
* get the genotype
*
* @return a map in lexigraphical order of the genotypes
*/
@Override
public Genotype getCallexGenotype() {
throw new UnsupportedOperationException("We don't support this right now");
}
/**
* get the genotypes
*
@ -273,29 +283,6 @@ public class RodVCF extends BasicReferenceOrderedDatum implements Variation, Var
return genotypes;
}
/**
* get the likelihoods
*
* @return an array in lexigraphical order of the likelihoods
*/
@Override
public Genotype getGenotype(DiploidGenotype x) {
if (x.toString().equals(getReference()))
return new BasicGenotype(this.getLocation(), getReference(), this.getReference().charAt(0), 0);
for (VCFGenotypeRecord record : mCurrentRecord.getVCFGenotypeRecords()) {
if (Utils.join("", record.getAlleles()).equals(x.toString())) {
double qual = 0.0;
if (record.getAlleles().equals(this.getReference()))
qual = this.getNegLog10PError();
else if (record.getFields().containsKey("GQ"))
qual = Double.valueOf(record.getFields().get("GQ")) / 10.0;
return new BasicGenotype(this.getLocation(), Utils.join("", record.getAlleles()), this.getReference().charAt(0), qual);
}
}
return null;
}
/**
* do we have the specified genotype? not all backedByGenotypes
* have all the genotype data.
@ -306,9 +293,7 @@ public class RodVCF extends BasicReferenceOrderedDatum implements Variation, Var
*/
@Override
public boolean hasGenotype(DiploidGenotype x) {
if (getGenotype(x) != null)
return true;
return false;
return (this.getAlternateBases().contains(x.toString()));
}
@Override

26
java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java
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@ -2,10 +2,7 @@ package org.broadinstitute.sting.gatk.refdata;
import net.sf.picard.util.SequenceUtil;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.genotype.BasicGenotype;
import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
import org.broadinstitute.sting.utils.genotype.VariantBackedByGenotype;
import org.broadinstitute.sting.utils.genotype.Variation;
import org.broadinstitute.sting.utils.genotype.*;
import java.util.ArrayList;
import java.util.Arrays;
@ -355,6 +352,16 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements Variation, V
return (int) (loc.getStop() - loc.getStart() + 1);
}
/**
* get the genotype
*
* @return a map in lexigraphical order of the genotypes
*/
@Override
public org.broadinstitute.sting.utils.genotype.Genotype getCallexGenotype() {
return new BasicGenotype(this.getLocation(), this.getAltBasesFWD(), this.getRefSnpFWD(), this.getConsensusConfidence());
}
/**
* get the likelihoods
*
@ -367,17 +374,6 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements Variation, V
return list;
}
/**
* get the likelihoods
*
* @return an array in lexigraphical order of the likelihoods
*/
@Override
public org.broadinstitute.sting.utils.genotype.Genotype getGenotype(DiploidGenotype x) {
if (!x.toString().equals(this.getAltBasesFWD())) throw new IllegalStateException("Unable to retrieve genotype");
return new BasicGenotype(this.getLocation(), this.getAltBasesFWD(), this.getRefSnpFWD(), this.getConsensusConfidence());
}
/**
* do we have the specified genotype? not all backedByGenotypes
* have all the genotype data.

12
java/src/org/broadinstitute/sting/utils/genotype/VariantBackedByGenotype.java
View File

@ -11,18 +11,18 @@ import java.util.List;
*/
public interface VariantBackedByGenotype {
/**
* get the likelihoods
* get the genotype
*
* @return a map in lexigraphical order of the likelihoods
* @return a specific genotype that represents the called genotype
*/
public List<Genotype> getGenotypes();
public Genotype getCallexGenotype();
/**
* get the likelihoods
* get the genotype
*
* @return a map in lexigraphical order of the likelihoods
* @return a map in lexigraphical order of the genotypes
*/
public Genotype getGenotype(DiploidGenotype x);
public List<Genotype> getGenotypes();
/**
* do we have the specified genotype? not all backedByGenotypes
* have all the genotype data.

29
java/test/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalkerIntegrationTest.java
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@ -114,7 +114,7 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest {
@Test
public void testEvalGenotypeROD() {
List<String> md5 = new ArrayList<String>();
md5.add("439c2983a6e1250cd845c686a0e5a085");
md5.add("d337f22057d2e9cfda03af3be70ce35a");
/**
* the above MD5 was calculated after running the following command:
*
@ -144,5 +144,32 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest {
md5);
List<File> result = executeTest("testEvalGenotypeROD", spec).getFirst();
}
@Test
public void testEvalMarksGenotypingExample() {
List<String> md5 = new ArrayList<String>();
md5.add("39ea64299cad44f816f033db54c8e622");
/**
* Run with the following commands:
*
* java -Xmx2048m -jar /humgen/gsa-hphome1/depristo/dev/GenomeAnalysisTK/trunk/dist/GenomeAnalysisTK.jar
* -T VariantEval -R /broad/1KG/reference/human_b36_both.fasta -l INFO
* -B eval,Variants,/humgen/gsa-scr1/ebanks/concordanceForMark/UMichVsBroad.venn.set1Only.calls
* -D /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -hc /humgen/gsa-scr1/GATK_Data/1KG_gffs/NA12878.1kg.gff
* -G -L 1 -o /humgen/gsa-scr1/ebanks/concordanceForMark/UMichVsBroad.venn.set1Only.calls.eval
*/
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T VariantEval -R /broad/1KG/reference/human_b36_both.fasta " +
"-B eval,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/UMichVsBroad.venn.set1Only.calls " +
"-D /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -hc /humgen/gsa-scr1/GATK_Data/1KG_gffs/NA12878.1kg.gff " +
"-G " +
"--supressDateInformation " +
"-L 1:1-10,000,000 " +
"--outerr %s",
1, // just one output file
md5);
List<File> result = executeTest("testEvalMarksGenotypingExample", spec).getFirst();
}
}