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Merge branch 'master' of github.com:broadinstitute/gsa-unstable

This commit is contained in:
Menachem Fromer 2013-05-06 13:52:55 -04:00
parent 13240588cf 98021db264
commit 86287dce76
2 changed files with 11 additions and 9 deletions
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3
protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordanceIntegrationTest.java
View File

@ -47,7 +47,6 @@
package org.broadinstitute.sting.gatk.walkers.variantutils; package org.broadinstitute.sting.gatk.walkers.variantutils;
import org.broadinstitute.sting.WalkerTest; import org.broadinstitute.sting.WalkerTest;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.testng.annotations.Test; import org.testng.annotations.Test;
import java.util.Arrays; import java.util.Arrays;
@ -87,7 +86,7 @@ public class GenotypeConcordanceIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
baseTestString("GenotypeConcordanceNonOverlapTest_Eval.vcf", "GenotypeConcordanceNonOverlapTest_Comp.vcf") + " -moltenize", baseTestString("GenotypeConcordanceNonOverlapTest_Eval.vcf", "GenotypeConcordanceNonOverlapTest_Comp.vcf") + " -moltenize",
0, 0,
Arrays.asList("370141088362d0ab7054be5249c49c11") Arrays.asList("3993709e38b033e89017dfbb63226e94")
); );
executeTest("Test moltenized output",spec); executeTest("Test moltenized output",spec);

17
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java
View File

@ -25,7 +25,10 @@
package org.broadinstitute.sting.gatk.walkers.variantutils; package org.broadinstitute.sting.gatk.walkers.variantutils;
import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Input;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@ -298,19 +301,19 @@ public class GenotypeConcordance extends RodWalker<List<Pair<VariantContext,Vari
String rowKey = String.format("%s_%s_%s",entry.getKey(),evalType.toString(),compType.toString()); String rowKey = String.format("%s_%s_%s",entry.getKey(),evalType.toString(),compType.toString());
concordanceCounts.set(rowKey,"Sample",entry.getKey()); concordanceCounts.set(rowKey,"Sample",entry.getKey());
concordanceCounts.set(rowKey,"Eval_Genotype",evalType.toString()); concordanceCounts.set(rowKey,"Eval_Genotype",evalType.toString());
concordanceCounts.set(rowKey,"Comp_Genotype",evalType.toString()); concordanceCounts.set(rowKey,"Comp_Genotype",compType.toString());
int count = table.get(evalType, compType); int count = table.get(evalType, compType);
concordanceCounts.set(rowKey,"Count",count); concordanceCounts.set(rowKey,"Count",count);
if ( evalType == GenotypeType.HET || evalType == GenotypeType.HOM_REF || evalType == GenotypeType.HOM_VAR) { if ( evalType == GenotypeType.HET || evalType == GenotypeType.HOM_REF || evalType == GenotypeType.HOM_VAR) {
concordanceEvalProportions.set(rowKey,"Sample",entry.getKey()); concordanceEvalProportions.set(rowKey,"Sample",entry.getKey());
concordanceEvalProportions.set(rowKey,"Eval_Genotype",evalType.toString()); concordanceEvalProportions.set(rowKey,"Eval_Genotype",evalType.toString());
concordanceEvalProportions.set(rowKey,"Comp_Genotype",evalType.toString()); concordanceEvalProportions.set(rowKey,"Comp_Genotype",compType.toString());
concordanceEvalProportions.set(rowKey,"Proportion",repairNaN(( (double) count)/table.getnEvalGenotypes(evalType))); concordanceEvalProportions.set(rowKey,"Proportion",repairNaN(( (double) count)/table.getnEvalGenotypes(evalType)));
} }
if ( compType == GenotypeType.HET || compType == GenotypeType.HOM_VAR || compType == GenotypeType.HOM_REF ) { if ( compType == GenotypeType.HET || compType == GenotypeType.HOM_VAR || compType == GenotypeType.HOM_REF ) {
concordanceCompProportions.set(rowKey,"Sample",entry.getKey()); concordanceCompProportions.set(rowKey,"Sample",entry.getKey());
concordanceCompProportions.set(rowKey,"Eval_Genotype",evalType.toString()); concordanceCompProportions.set(rowKey,"Eval_Genotype",evalType.toString());
concordanceCompProportions.set(rowKey,"Comp_Genotype",evalType.toString()); concordanceCompProportions.set(rowKey,"Comp_Genotype",compType.toString());
concordanceCompProportions.set(rowKey,"Proportion",repairNaN(( (double) count)/table.getnCompGenotypes(compType))); concordanceCompProportions.set(rowKey,"Proportion",repairNaN(( (double) count)/table.getnCompGenotypes(compType)));
} }
} }
@ -337,19 +340,19 @@ public class GenotypeConcordance extends RodWalker<List<Pair<VariantContext,Vari
String rowKey = String.format("%s_%s_%s",sampleKey,evalType.toString(),compType.toString()); String rowKey = String.format("%s_%s_%s",sampleKey,evalType.toString(),compType.toString());
concordanceCounts.set(rowKey,"Sample",sampleKey); concordanceCounts.set(rowKey,"Sample",sampleKey);
concordanceCounts.set(rowKey,"Eval_Genotype",evalType.toString()); concordanceCounts.set(rowKey,"Eval_Genotype",evalType.toString());
concordanceCounts.set(rowKey,"Comp_Genotype",evalType.toString()); concordanceCounts.set(rowKey,"Comp_Genotype",compType.toString());
int count = table.get(evalType, compType); int count = table.get(evalType, compType);
concordanceCounts.set(rowKey,"Count",count); concordanceCounts.set(rowKey,"Count",count);
if ( evalType == GenotypeType.HET || evalType == GenotypeType.HOM_REF || evalType == GenotypeType.HOM_VAR) { if ( evalType == GenotypeType.HET || evalType == GenotypeType.HOM_REF || evalType == GenotypeType.HOM_VAR) {
concordanceEvalProportions.set(rowKey,"Sample",sampleKey); concordanceEvalProportions.set(rowKey,"Sample",sampleKey);
concordanceEvalProportions.set(rowKey,"Eval_Genotype",evalType.toString()); concordanceEvalProportions.set(rowKey,"Eval_Genotype",evalType.toString());
concordanceEvalProportions.set(rowKey,"Comp_Genotype",evalType.toString()); concordanceEvalProportions.set(rowKey,"Comp_Genotype",compType.toString());
concordanceEvalProportions.set(rowKey,"Proportion",repairNaN(( (double) count)/table.getnEvalGenotypes(evalType))); concordanceEvalProportions.set(rowKey,"Proportion",repairNaN(( (double) count)/table.getnEvalGenotypes(evalType)));
} }
if ( compType == GenotypeType.HET || compType == GenotypeType.HOM_VAR || compType == GenotypeType.HOM_REF ) { if ( compType == GenotypeType.HET || compType == GenotypeType.HOM_VAR || compType == GenotypeType.HOM_REF ) {
concordanceCompProportions.set(rowKey,"Sample",sampleKey); concordanceCompProportions.set(rowKey,"Sample",sampleKey);
concordanceCompProportions.set(rowKey,"Eval_Genotype",evalType.toString()); concordanceCompProportions.set(rowKey,"Eval_Genotype",evalType.toString());
concordanceCompProportions.set(rowKey,"Comp_Genotype",evalType.toString()); concordanceCompProportions.set(rowKey,"Comp_Genotype",compType.toString());
concordanceCompProportions.set(rowKey,"Proportion",repairNaN(( (double) count)/table.getnCompGenotypes(compType))); concordanceCompProportions.set(rowKey,"Proportion",repairNaN(( (double) count)/table.getnCompGenotypes(compType)));
} }
} }