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Prints 0.0 TiTv not NaN when there are no variants 

-- Updated md5
This commit is contained in:
Mark DePristo 2011-12-07 12:07:54 -05:00
parent e17a1923fb
commit 4055877708
2 changed files with 6 additions and 5 deletions
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3
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java
View File

@ -144,7 +144,8 @@ public class VariantSummary extends VariantEvaluator implements StandardEval {
n++;
}
}
return sum / (1.0 * n);
return n > 0 ? sum / (1.0 * n) : 0.0;
}
}

8
public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
View File

@ -277,7 +277,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
" --eval " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" +
" --comp:comp_genotypes,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.head.vcf";
WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -ST CpG -o %s",
1, Arrays.asList("6fa6e77f149de3d13c31d410a98043a0"));
1, Arrays.asList("4f60acc8a4b21c4b4ccb51ad9071449c"));
executeTestParallel("testSelect1", spec);
}
@ -294,7 +294,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
@Test
public void testCompVsEvalAC() {
String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -ST CpG -EV GenotypeConcordance --eval:evalYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.very.few.lines.vcf --comp:compYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.fake.genotypes.ac.test.vcf";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("aeff16bb43be03a2a7e5b9d0108b4999"));
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("fa13eb59892892c07711c6ffe31bf870"));
executeTestParallel("testCompVsEvalAC",spec);
}
@ -324,7 +324,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
" --dbsnp " + b37dbSNP132 +
" --eval:evalBI " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
" -noST -ST Novelty -o %s";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("38ed9d216bd43f1cceceea24146fae38"));
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("190e1a171132832bf92fbca56a9c40bb"));
executeTestParallel("testEvalTrackWithoutGenotypes",spec);
}
@ -336,7 +336,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
" --eval:evalBI " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
" --eval:evalBC " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bc.sites.vcf" +
" -noST -ST Novelty -o %s";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("453c6b1f7165913e8b1787e22bac1281"));
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("08586d443fdcf3b7f63b8f9e3a943c62"));
executeTestParallel("testMultipleEvalTracksWithoutGenotypes",spec);
}