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Ensure output table formatting does not contain NaNs. For (0 eval ref calls)/(0 comp ref calls), set the proportion to 0.00. 

Added integration tests (checked against manual tabulation)
This commit is contained in:
Chris Hartl 2013-01-14 09:21:30 -05:00
parent 1b535f6d91
commit 61bc334df1
2 changed files with 79 additions and 9 deletions
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25
protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java
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@ -85,6 +85,13 @@ public class GenotypeConcordance extends RodWalker<Pair<VariantContext,VariantCo
return metrics;
}
private static double repairNaN(double d) {
if ( Double.isNaN(d) ) {
return 0.0;
}
return d;
}
public void onTraversalDone(ConcordanceMetrics metrics) {
GATKReport report = new GATKReport();
GATKReportTable concordanceCounts = new GATKReportTable("GenotypeConcordance_Counts","Per-sample concordance tables: comparison counts",2+GenotypeType.values().length*GenotypeType.values().length);
@ -126,13 +133,13 @@ public class GenotypeConcordance extends RodWalker<Pair<VariantContext,VariantCo
int count = table.get(evalType, compType);
concordanceCounts.set(entry.getKey(),colKey,count);
if ( evalType == GenotypeType.HET || evalType == GenotypeType.HOM_REF || evalType == GenotypeType.HOM_VAR)
concordanceEvalProportions.set(entry.getKey(),colKey,( (double) count)/table.getnEvalGenotypes(evalType));
concordanceEvalProportions.set(entry.getKey(),colKey,repairNaN(( (double) count)/table.getnEvalGenotypes(evalType)));
if ( compType == GenotypeType.HET || compType == GenotypeType.HOM_VAR || compType == GenotypeType.HOM_REF )
concordanceCompProportions.set(entry.getKey(),colKey,( (double) count)/table.getnCompGenotypes(compType));
concordanceCompProportions.set(entry.getKey(),colKey,repairNaN(( (double) count)/table.getnCompGenotypes(compType)));
}
}
concordanceEvalProportions.set(entry.getKey(),"Mismatching_Alleles", ( (double) table.getnMismatchingAlt() )/table.getnCalledEvalGenotypes());
concordanceCompProportions.set(entry.getKey(),"Mismatching_Alleles", ( (double) table.getnMismatchingAlt() )/table.getnCalledCompGenotypes());
concordanceEvalProportions.set(entry.getKey(),"Mismatching_Alleles", repairNaN(( (double) table.getnMismatchingAlt() )/table.getnCalledEvalGenotypes()));
concordanceCompProportions.set(entry.getKey(),"Mismatching_Alleles", repairNaN(( (double) table.getnMismatchingAlt() )/table.getnCalledCompGenotypes()));
concordanceCounts.set(entry.getKey(),"Mismatching_Alleles",table.getnMismatchingAlt());
}
@ -147,13 +154,13 @@ public class GenotypeConcordance extends RodWalker<Pair<VariantContext,VariantCo
int count = table.get(evalType,compType);
concordanceCounts.set(rowKey,colKey,count);
if ( evalType == GenotypeType.HET || evalType == GenotypeType.HOM_REF || evalType == GenotypeType.HOM_VAR)
concordanceEvalProportions.set(rowKey,colKey,( (double) count)/table.getnEvalGenotypes(evalType));
concordanceEvalProportions.set(rowKey,colKey,repairNaN(( (double) count)/table.getnEvalGenotypes(evalType)));
if ( compType == GenotypeType.HET || compType == GenotypeType.HOM_VAR || compType == GenotypeType.HOM_REF )
concordanceCompProportions.set(rowKey,colKey,( (double) count)/table.getnCompGenotypes(compType));
concordanceCompProportions.set(rowKey,colKey,repairNaN(( (double) count)/table.getnCompGenotypes(compType)));
}
}
concordanceEvalProportions.set(rowKey,"Mismatching_Alleles", ( (double) table.getnMismatchingAlt() )/table.getnCalledEvalGenotypes());
concordanceCompProportions.set(rowKey,"Mismatching_Alleles", ( (double) table.getnMismatchingAlt() )/table.getnCalledCompGenotypes());
concordanceEvalProportions.set(rowKey,"Mismatching_Alleles", repairNaN(( (double) table.getnMismatchingAlt() )/table.getnCalledEvalGenotypes()));
concordanceCompProportions.set(rowKey,"Mismatching_Alleles", repairNaN(( (double) table.getnMismatchingAlt() )/table.getnCalledCompGenotypes()));
concordanceCounts.set(rowKey,"Mismatching_Alleles",table.getnMismatchingAlt());
for ( Map.Entry<String,Double> nrsEntry : metrics.getPerSampleNRS().entrySet() ) {
@ -210,4 +217,4 @@ public class GenotypeConcordance extends RodWalker<Pair<VariantContext,VariantCo
builder.genotypes(newGeno);
return builder.make();
}
}
}

63
protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordanceIntegrationTest.java 100644
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@ -0,0 +1,63 @@
/*
* Copyright (c) 2010.
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.walkers.variantutils;
import org.broadinstitute.sting.WalkerTest;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.testng.annotations.Test;
import java.util.Arrays;
public class GenotypeConcordanceIntegrationTest extends WalkerTest {
protected static final String emptyMd5 = "d41d8cd98f00b204e9800998ecf8427e";
public static String baseTestString(String eval, String comp) {
return "-T GenotypeConcordance -R " + b37KGReference + " --eval " + validationDataLocation + eval + " --comp " + validationDataLocation + comp + " -o %s";
}
@Test
public void testIndelConcordance() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString("NA12878.Jan2013.haplotypeCaller.subset.indels.vcf", "NA12878.Jan2013.bestPractices.subset.indels.vcf"),
0,
Arrays.asList("0f29a0c6dc44066228c8cb204fd53ec0")
);
executeTest("test indel concordance", spec);
}
@Test
public void testNonoverlapingSamples() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString("GenotypeConcordanceNonOverlapTest_Eval.vcf", "GenotypeConcordanceNonOverlapTest_Comp.vcf"),
0,
Arrays.asList("fc725022d47b4b5f8a6ef87f0f1ffe89")
);
executeTest("test non-overlapping samples", spec);
}
}