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Removing HWP from GenotypeSummaries because of integer overflow issues with 91K samples. Removing CCC because it is redundant.

This commit is contained in:
Ryan Poplin 2014-05-27 09:59:52 -04:00
parent 3696c2d817
commit b24cff780b
3 changed files with 8 additions and 12 deletions
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2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/GenotypeSummaries.java
View File

@ -89,9 +89,7 @@ public class GenotypeSummaries extends InfoFieldAnnotation implements ActiveRegi
return null;
final Map<String,Object> returnMap = new HashMap<>();
returnMap.put(CCC, vc.getCalledChrCount());
returnMap.put(NCC, vc.getNoCallCount());
returnMap.put(HWP, String.format("%.4f", GATKVariantContextUtils.computeHardyWeinbergPvalue(vc)));
final MathUtils.RunningAverage average = new MathUtils.RunningAverage();
for( final Genotype g : vc.getGenotypes() ) {

2
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/GenotypeSummariesUnitTest.java
View File

@ -77,10 +77,8 @@ public class GenotypeSummariesUnitTest {
final GenotypeSummaries GS = new GenotypeSummaries();
final Map<String,Object> resultMap = GS.annotate(null, null, null, null, testVC, null);
Assert.assertEquals(2, resultMap.get(GenotypeSummaries.CCC)); // 2 called chromosomes
Assert.assertEquals(1, resultMap.get(GenotypeSummaries.NCC)); // 1 no-called called sample
Assert.assertEquals(30.0, Double.parseDouble((String)resultMap.get(GenotypeSummaries.GQ_MEAN)), 1E-4); // mean GQ is 30
Assert.assertFalse(resultMap.containsKey(GenotypeSummaries.GQ_STDDEV)); // no stddev with only one data point
Assert.assertTrue(resultMap.containsKey(GenotypeSummaries.HWP));
}
}

16
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
View File

@ -65,7 +65,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
" -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
" -L 20:10,000,000-20,000,000", b37KGReference),
1,
Arrays.asList("09575e44c9dbcd171a30eff43961c57f"));
Arrays.asList("51bf72a5eb3b2592d319072e4ce26c92"));
executeTest("combineSingleSamplePipelineGVCF", spec);
}
@ -77,7 +77,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
" -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
" --includeNonVariantSites -L 20:10,030,000-10,033,000 -L 20:10,386,000-10,386,500", b37KGReference),
1,
Arrays.asList("fc701a483e7f0672f8c9a189c7b53015"));
Arrays.asList("4200fce6f253ef51dc4cd903794270b9"));
executeTest("combineSingleSamplePipelineGVCF_includeNonVariants", spec);
}
@ -90,7 +90,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
" -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
" -L 20:10,000,000-20,000,000", b37KGReference),
1,
Arrays.asList("3f34e05318479cf8743f4227491c7cd1"));
Arrays.asList("46044467b366db1c15a48a429b7c2291"));
executeTest("combineSingleSamplePipelineGVCFHierarchical", spec);
}
@ -102,7 +102,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
" -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
" -L 20:10,000,000-11,000,000 --dbsnp " + b37dbSNP132, b37KGReference),
1,
Arrays.asList("dc13542c71fbb4846507b0cdcc4827be"));
Arrays.asList("52655b4a693bc79e1029e47276a2653b"));
executeTest("combineSingleSamplePipelineGVCF_addDbsnp", spec);
}
@ -112,7 +112,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
"-T GenotypeGVCFs --no_cmdline_in_header -L 1:69485-69791 -o %s -R " + b37KGReference +
" -V " + privateTestDir + "gvcfExample1.vcf",
1,
Arrays.asList("afff9f7b03008214ad41d430d57bb541"));
Arrays.asList("6fe339b17f4e5621e849d842c64a6e42"));
executeTest("testJustOneSample", spec);
}
@ -123,7 +123,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
" -V " + privateTestDir + "gvcfExample1.vcf" +
" -V " + privateTestDir + "gvcfExample2.vcf",
1,
Arrays.asList("2b0f8662be950e49911dfd2d93776712"));
Arrays.asList("aad7bda0f3c60689b61e87d641b62856"));
executeTest("testSamplesWithDifferentLs", spec);
}
@ -134,12 +134,12 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
"-T GenotypeGVCFs --no_cmdline_in_header -L 1:1115550-1115551 -o %s -R " + hg19Reference +
" --variant " + privateTestDir + "combined_genotype_gvcf_exception.vcf",
1,
Arrays.asList("97bf0aad80b3992704166bbaca0cc455"));
Arrays.asList("1dda31e020086a4c5643571fbccd40ba"));
WalkerTestSpec spec2 = new WalkerTestSpec(
"-T GenotypeGVCFs --no_cmdline_in_header -L 1:1115550-1115551 -o %s -R " + hg19Reference +
" --variant " + privateTestDir + "combined_genotype_gvcf_exception.nocall.vcf",
1,
Arrays.asList("97bf0aad80b3992704166bbaca0cc455"));
Arrays.asList("1dda31e020086a4c5643571fbccd40ba"));
executeTest("testNoPLsException.1", spec1);
executeTest("testNoPLsException.2", spec2);
}