diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFs.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFs.java index feb2fbb2e..7e716a979 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFs.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFs.java @@ -133,6 +133,9 @@ import java.util.*; @Reference(window=@Window(start=-10,stop=10)) @SuppressWarnings("unused") public class GenotypeGVCFs extends RodWalker implements AnnotatorCompatible, TreeReducible { + + private static String GVCF_BLOCK = "GVCFBlock"; + /** * The gVCF files to merge together */ @@ -229,6 +232,14 @@ public class GenotypeGVCFs extends RodWalker headerLines = VCFUtils.smartMergeHeaders(vcfRods.values(), true); + + // Remove GCVFBlocks + for ( final Iterator iter = headerLines.iterator(); iter.hasNext(); ) { + if ( iter.next().getKey().contains(GVCF_BLOCK) ) { + iter.remove(); + } + } + headerLines.addAll(annotationEngine.getVCFAnnotationDescriptions()); headerLines.addAll(genotypingEngine.getAppropriateVCFInfoHeaders()); diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java index cb903ba79..659d6e2d5 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java @@ -83,7 +83,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { final WalkerTestSpec spec = new WalkerTestSpec( baseTestString(" -V " + privateTestDir + "testUpdatePGT.vcf", b37KGReference), 1, - Collections.singletonList("8d9788afd0de26bd9d9e55dd0e9fc3ed")); + Collections.singletonList("de36b46bc523b305bf344591a285c0d9")); executeTest("testUpdatePGT", spec); } @@ -93,7 +93,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { final WalkerTestSpec spec = new WalkerTestSpec( baseTestString(" -V " + privateTestDir + "testUpdatePGT.vcf -A StrandAlleleCountsBySample -log " + logFileName, b37KGReference), 1, - Collections.singletonList("5dd4698da963a423446bb1e183eb75aa")); + Collections.singletonList("c8eba89f434ca5e9dc0f157bcd4bea11")); executeTest("testUpdatePGTStrandAlleleCountsBySample", spec); final File file = new File(logFileName); @@ -108,7 +108,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { " -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" + " -L 20:10,000,000-11,000,000", b37KGReference), 1, - Collections.singletonList("61dd2aaabf94a8f5b87d5069a75d84d7")); + Collections.singletonList("b82f29eee8b1369b376ace857bf9b55a")); executeTest("combineSingleSamplePipelineGVCF", spec); } @@ -120,7 +120,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { " -V:sample3 " + privateTestDir + "tetraploid-gvcf-3.vcf" + " -L " + privateTestDir + "tetraploid-gvcfs.intervals", b37KGReference), 1, - Collections.singletonList("64fa89f20ee25df21ad20ce4ada7e7ad")); + Collections.singletonList("d6ef5e411ac5829a12d825a0fefac883")); executeTest("testTetraploidRun", spec); } @@ -132,7 +132,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { " -V:sample3 " + privateTestDir + "diploid-gvcf-3.vcf" + " -L " + privateTestDir + "tetraploid-gvcfs.intervals", b37KGReference), 1, - Collections.singletonList("b1d93f4cd93093c208be2c9842f38d12")); + Collections.singletonList("b497f16cd9eb99e353d9430fe7f34635")); executeTest("testMixedPloidyRun", spec); } @@ -145,7 +145,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { " -L " + privateTestDir + "tetraploid-gvcfs.intervals" + " -maxNumPLValues 3", b37KGReference), 1, - Collections.singletonList("c0dcf62fb116c4c0baabe432eceea52c")); + Collections.singletonList("8c8ebe2069977ba13024a95827c6c50d")); executeTest("testMixedPloidyMaxNumPLValuesRun", spec); } @@ -157,7 +157,7 @@ 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, - Collections.singletonList("af19ee0d7e739143be4e252c48701c45")); + Collections.singletonList("edf083b3bf9cdec31b997a70fd56a7b2")); executeTest("combineSingleSamplePipelineGVCF_includeNonVariants", spec); } @@ -170,7 +170,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { " -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" + " -L 20:10,000,000-20,000,000", b37KGReference), 1, - Collections.singletonList("3943e70eed48618040469e157509868e")); + Collections.singletonList("b304c7e3bb3625a1cdb5531c77b13bcd")); executeTest("combineSingleSamplePipelineGVCFHierarchical", spec); } @@ -182,7 +182,7 @@ 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, - Collections.singletonList("51d498327342bd3b0b092845b437aad5")); + Collections.singletonList("08adc638b9539fd275836ed008d900ee")); executeTest("combineSingleSamplePipelineGVCF_addDbsnp", spec); } @@ -203,7 +203,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { "-T GenotypeGVCFs --no_cmdline_in_header -L 1:69485-69791 -o %s -R " + b37KGReference + " -V " + privateTestDir + "gvcfExample1.vcf", 1, - Collections.singletonList("9ff344a5ab87a2c3b128e435e2e86db0")); + Collections.singletonList("df88bbf2eea39a06f2bcc47d9379e5fa")); executeTest("testJustOneSample", spec); } @@ -214,14 +214,14 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { " -V " + privateTestDir + "gvcfExample1.vcf" + " -V " + privateTestDir + "gvcfExample2.vcf", 1, - Collections.singletonList("0c07ed795562ea96eab427e63a970384")); + Collections.singletonList("933c3ec48870c54f7f74b259272d6645")); executeTest("testSamplesWithDifferentLs", spec); } @Test public void testNoPLsException() { // Test with input files with (1) 0/0 and (2) ./. - final String md5 = "2f3d71272fdac19ac861cc7159edfb08"; + final String md5 = "91038469a8133feb05038528f8565840"; final WalkerTestSpec spec1 = new WalkerTestSpec( "-T GenotypeGVCFs --no_cmdline_in_header -L 1:1115550-1115551 -o %s -R " + hg19Reference + " --variant " + privateTestDir + "combined_genotype_gvcf_exception.vcf", @@ -282,7 +282,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { final WalkerTestSpec spec = new WalkerTestSpec( baseTestString(" -V " + gVCF.getAbsolutePath(), b37KGReference), 1, - Collections.singletonList("7dfe841940c63415bd5d07ae5d0c69d7")); + Collections.singletonList("8a6e69c8d0b4dd9bf0646173f1b1f32c")); spec.disableShadowBCF(); //TODO: Remove when BaseTest.assertAttributesEquals() works with SAC executeTest("testStrandAlleleCountsBySample", spec); } @@ -299,7 +299,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { " -V:combined2 " + privateTestDir + "combine.single.sample.pipeline.combined.vcf" + " --uniquifySamples", b37KGReference), 1, - Collections.singletonList("c23b1e3f9a960e022038768998a8df82")); + Collections.singletonList("1cb3bddf47c620d294b08acd70d35fa3")); executeTest("testUniquifiedSamples", spec); } @@ -471,7 +471,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { } - private static final String simpleSpanningDeletionsMD5 = "4629c2f02ff58c111828269091cded82"; + private static final String simpleSpanningDeletionsMD5 = "53f2b8991e49a47efc44b8e02ebb8d91"; @Test public void testSpanningDeletionsMD5() { @@ -501,7 +501,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference + " -V " + privateTestDir + "spanningDel.1.g.vcf -V " + privateTestDir + "spanningDel.2.g.vcf -V " + privateTestDir + "spanningDel.3.g.vcf", 1, - Collections.singletonList("7fe5364565585d31a0bb6a9dfa4a01d4")); + Collections.singletonList("907dfaa4d31c22705eadd5890ae23929")); spec.disableShadowBCF(); executeTest("testMultipleSpanningDeletionsMD5", spec); } @@ -512,7 +512,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference + " -V " + privateTestDir + "spanningDel.delOnly.g.vcf", 1, - Collections.singletonList("057f9368f380bf3c12b539a749deac61")); + Collections.singletonList("b923e5c6d5dbce62034178bd5234b932")); spec.disableShadowBCF(); executeTest("testSpanningDeletionDoesNotGetGenotypedWithNoOtherAlleles", spec); } @@ -523,7 +523,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference + " -V " + privateTestDir + "spanningDel.depr.delOnly.g.vcf", 1, - Collections.singletonList("e8f5186718050fe0784416e41425563f")); + Collections.singletonList("01ae75dfe5c0c2350fcef0f4cdca36b2")); spec.disableShadowBCF(); executeTest("testSpanningDeletionDoesNotGetGenotypedWithNoOtherAlleles", spec); } @@ -546,7 +546,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference + " -V " + privateTestDir + "ad-bug-input.vcf", 1, - Collections.singletonList("5ed5cb6aac68aa8943dc45b8b90eb508")); + Collections.singletonList("4d6cbd8d666a43fc136d73de2b217719")); spec.disableShadowBCF(); executeTest("testBadADPropagationHaploidBugTest", spec); } @@ -557,7 +557,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference + " -V " + privateTestDir + "261_S01_raw_variants_gvcf.vcf", 1, - Collections.singletonList("37eec6aedd26aa3430a15d90d7f8a011")); + Collections.singletonList("ea96440b537dd1b2b25ea565dfaa71fc")); spec.disableShadowBCF(); executeTest("testSAC", spec); } @@ -568,7 +568,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference + " -V " + privateTestDir + "tetraploid-multisample-sac.g.vcf", 1, - Collections.singletonList("76532a74d4ba49f23362c149ad31a229")); + Collections.singletonList("c21c847ef794c11e249985a16893b2fa")); spec.disableShadowBCF(); executeTest("testSACMultisampleTetraploid", spec); } @@ -579,7 +579,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { baseTestString(" -V " + privateTestDir + "set.zero.RGQs.no.call.sample1.g.vcf" + " -V " + privateTestDir + "set.zero.RGQs.no.call.sample2.g.vcf" + " -L chr16:1279274-1279874 -allSites", hg19ReferenceWithChrPrefixInChromosomeNames), - Collections.singletonList("92c097d8b6074d40f8d1385bc92a0a5d")); + Collections.singletonList("fc7016c0cd5cfa186bab80329eb0bc13")); spec.disableShadowBCF(); executeTest("testSetZeroRGQsToNoCall", spec); } @@ -588,7 +588,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { public void testAlleleSpecificAnnotations() { final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard --disableDithering -V " + privateTestDir + "NA12878.AS.chr20snippet.g.vcf -V " + privateTestDir + "NA12891.AS.chr20snippet.g.vcf"; - final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("89712a9fe5b6db16be2257be2b0b4759")); + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("29d6db0a93abd72d64fb1e82da65c715")); spec.disableShadowBCF(); executeTest("testAlleleSpecificAnnotations", spec); } @@ -597,7 +597,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { public void testASMateRankSumAnnotation() { final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard -A AS_MQMateRankSumTest --disableDithering -V " + privateTestDir + "NA12878.AS.MateRankSum.chr20snippet.g.vcf -V " + privateTestDir + "NA12891.AS.MateRankSum.chr20snippet.g.vcf"; - final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("8e41a139600ab58a67910cdc60053726")); + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("2a330015a7db9f9aee9bc5b776698f73")); spec.disableShadowBCF(); executeTest("testASMateRankSumAnnotation", spec); } @@ -606,7 +606,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { public void testASInsertSizeRankSumAnnotation() { final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard --disableDithering -V " + privateTestDir + "NA12878.AS.InsertSizeRankSum.chr20snippet.g.vcf -V " + privateTestDir + "NA12891.AS.InsertSizeRankSum.chr20snippet.g.vcf"; - final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("b1334fbfbf21934aac1c1eda0b5062d5")); + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("75aee1e0c8c3528180e344ec6c0d8ffd")); spec.disableShadowBCF(); executeTest("testASInsertSizeRankSumAnnotation", spec); } @@ -619,7 +619,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { public void testAlleleSpecificAnnotations_oneSample() { final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard --disableDithering -V " + privateTestDir + "NA12878.AS.chr20snippet.g.vcf"; - final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("7d86260e91fe74588e01339a2064b59c")); + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("f4fa3acec2b21037368898e913b7a3fa")); spec.disableShadowBCF(); executeTest("testAlleleSpecificAnnotations_oneSample", spec); } @@ -629,7 +629,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { public void testAlleleSpecificAnnotations_elevenSamples() { final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard --disableDithering -V " + privateTestDir + "multiSamples.g.vcf"; - final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("a889fe6775575513e84905b4fa98f8b3")); + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("4e90f6908248fac9b3ce3e545180a8e5")); spec.disableShadowBCF(); executeTest("testAlleleSpecificAnnotations_elevenSamples", spec); } @@ -638,7 +638,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { public void testMonomorphicVCwithAlt() { final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -G AS_Standard -o %s --no_cmdline_in_header --disableDithering -V " + privateTestDir + "monomorphicGVCwithAlt.vcf"; - final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("8bf329a40637623515972dcc0e09a49e")); + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("43953b3e75a4d470b65773b1b5bea066")); spec.disableShadowBCF(); executeTest("testAlleleSpecificAnnotations", spec); } @@ -647,7 +647,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { public void testFractionInformativeReads() { final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -G AS_Standard -o %s --no_cmdline_in_header -A FractionInformativeReads --disableDithering -V " + privateTestDir + "NA12878.AS.chr20snippet.g.vcf -V " + privateTestDir + "NA12891.AS.chr20snippet.g.vcf"; - final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("b338bf1807791b23255b8cb1947c01b2")); + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("0b1bbcc7d24f8b0945c97907b1cdd974")); spec.disableShadowBCF(); executeTest("testAlleleSpecificAnnotations", spec); } @@ -657,7 +657,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { public void testGenotypingSpanningDeletionWithAllSites() { final WalkerTestSpec spec = new WalkerTestSpec( baseTestString(" -V " + privateTestDir + "spanningDel.genotyping.g.vcf -allSites", b37KGReference), - Collections.singletonList("7cc3b08a37ed0c2e556debc1023cff2b")); + Collections.singletonList("e2370ba728cc9b73950b2ed616ef669f")); spec.disableShadowBCF(); executeTest("testGenotypingSpanningDeletionWithAllSites", spec); } @@ -666,7 +666,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { public void testGenotypingSpanningDeletionAcrossLines() { final WalkerTestSpec spec = new WalkerTestSpec( baseTestString(" -V " + privateTestDir + "input-1_2256566.vcf", b37KGReference), - Collections.singletonList("24ac243e77e679508c6554194923317b")); + Collections.singletonList("152c8e07e35c592868f43626f27365de")); spec.disableShadowBCF(); executeTest("testGenotypingSpanningDeletionAcrossLines", spec); }