From b39508cd159d6c285a5d1f3e63eb10683655a2c3 Mon Sep 17 00:00:00 2001 From: Valentin Ruano-Rubio Date: Mon, 11 Aug 2014 17:47:25 -0400 Subject: [PATCH] ReadLikelihoods class introduction final changes before merging Stories: https://www.pivotaltracker.com/story/show/70222086 https://www.pivotaltracker.com/story/show/67961652 Changes: Done some changes that I missed in relation with making sure that all PairHMM implentations use the same interface; as a consequence we were running always the standard PairHMM. Fixed some additional bugs detected when running it on full wgs single sample and exom multi sample data set. Updated some integration test md5s. --- .../walkers/indels/PairHMMIndelErrorModel.java | 4 ++-- ...enotyperGeneralPloidySuite1IntegrationTest.java | 2 +- ...enotyperGeneralPloidySuite2IntegrationTest.java | 2 +- ...nifiedGenotyperIndelCallingIntegrationTest.java | 14 +++++++------- ...ifiedGenotyperNormalCallingIntegrationTest.java | 8 ++++---- 5 files changed, 15 insertions(+), 15 deletions(-) diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/PairHMMIndelErrorModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/PairHMMIndelErrorModel.java index a2422c544..6f71868bb 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/PairHMMIndelErrorModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/PairHMMIndelErrorModel.java @@ -447,8 +447,8 @@ public class PairHMMIndelErrorModel { final List distinctHaplotypesList = Arrays.asList(distinctHaplotypesSet.toArray(new Haplotype[distinctHaplotypesSet.size()])); // Get the likelihoods for our clipped read against each of our trimmed haplotypes. final ReadLikelihoods rl = new ReadLikelihoods<>( - Collections.singletonList("DUMMY_SAMPLE"),distinctHaplotypesList,Collections.singletonMap("DUMMY_SAMPLE",Collections.singletonList(processedRead))); + final ReadLikelihoods.Matrix dummySampleLikelihoods = rl.sampleMatrix(0); pairHMM.computeLikelihoods(rl.sampleMatrix(0), Collections.singletonList(processedRead), readGCPArrayMap); @@ -458,7 +458,7 @@ public class PairHMMIndelErrorModel { final int hIndex = rl.alleleIndex(h); final double readLikelihood = dummySampleLikelihoods.get(hIndex,0); readLikelihoods[readIdx][j++] = readLikelihood; - perReadAlleleLikelihoodMap.add(read,a,readLikelihood); + perReadAlleleLikelihoodMap.add(p,a,readLikelihood); } } } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java index 3d6103966..7ac0c86df 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java @@ -79,6 +79,6 @@ public class UnifiedGenotyperGeneralPloidySuite1IntegrationTest extends WalkerTe @Test(enabled = true) public void testINDEL_maxAltAlleles2_ploidy1_Pools_noRef() { - executor.PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1", "LSV_INDEL_DISC_NOREF_p1", "INDEL", "a9730f883a2e01e93d56b11321c9fd52"); + executor.PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1", "LSV_INDEL_DISC_NOREF_p1", "INDEL", "ae90d6be28c19e455083a47bc95c3b1b"); } } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java index 98a1586f9..6d95098fe 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java @@ -58,7 +58,7 @@ public class UnifiedGenotyperGeneralPloidySuite2IntegrationTest extends WalkerTe @Test(enabled = true) public void testINDEL_maxAltAlleles2_ploidy3_Pools_noRef() { - executor.PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","93cf7ed2645599d0ddd319c6989eadcc"); + executor.PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","9fc4f04105bde31bafc93548745cb67e"); } @Test(enabled = true) diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java index 286096111..e8971f820 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java @@ -73,7 +73,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest { " -o %s" + " -L 1:10,000,000-10,500,000", 1, - Arrays.asList("24d5f65860507ec7f8d9441bfee8653a")); + Arrays.asList("8a4de9e1f59cffe80a4372cf02fe809e")); executeTest(String.format("test indel caller in SLX"), spec); } @@ -100,7 +100,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest { " -o %s" + " -L 1:10,000,000-10,500,000", 1, - Arrays.asList("188dc4d70dc5f4de09f645270cc3f4e1")); + Arrays.asList("2b92df91a9337b9d9f03db5699bb41f2")); executeTest(String.format("test indel calling, multiple technologies"), spec); } @@ -110,7 +110,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "indelAllelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1, - Arrays.asList("31aaad9adbf12bb7fb12d53080e5c2f5")); + Arrays.asList("591c9a7bd7d64974b4a2dd932fdef138")); executeTest("test MultiSample Pilot2 indels with alleles passed in", spec); } @@ -120,7 +120,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest { baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "indelAllelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1, - Arrays.asList("fecb8ae4e8f5ea2b2bf3826d674298f7")); + Arrays.asList("e784b6d1b3725f72a2c42b19e8d24cb1")); executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec); } @@ -135,7 +135,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec( baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + result.get(0).getAbsolutePath() + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L " + result.get(0).getAbsolutePath(), 1, - Arrays.asList("0662ec6fe6d6e9807f758b1c82adf056")); + Arrays.asList("d101beb3d1f71a14a31438cce9786881")); executeTest("test MultiSample Pilot1 CEU indels using GENOTYPE_GIVEN_ALLELES", spec2); } @@ -176,7 +176,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest { public void testMinIndelFraction0() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( assessMinIndelFraction + " -minIndelFrac 0.0", 1, - Arrays.asList("3d5140ffc02a125ee26c63ec55449192")); + Arrays.asList("96c2ab043f523c7676e4bc36dd3c9d0b")); executeTest("test minIndelFraction 0.0", spec); } @@ -184,7 +184,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest { public void testMinIndelFraction25() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( assessMinIndelFraction + " -minIndelFrac 0.25", 1, - Arrays.asList("7c62eb9142d9124e49c123dcc052ce57")); + Arrays.asList("53ce3aa9ee16302ab2ec21f742b5e157")); executeTest("test minIndelFraction 0.25", spec); } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java index 8398b1776..8e5b9aa68 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java @@ -65,7 +65,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{ public void testMultiSamplePilot1() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000", 1, - Arrays.asList("c6462121e5a419546f50d53646274fd3")); + Arrays.asList("058b54cff14527485c7b1ab035ebb6c4")); executeTest("test MultiSample Pilot1", spec); } @@ -97,7 +97,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{ public void testMultipleSNPAlleles() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper --contamination_fraction_to_filter 0.05 --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + privateTestDir + "multiallelic.snps.bam -o %s -L " + privateTestDir + "multiallelic.snps.intervals", 1, - Arrays.asList("85e8ba3cfeef5e3b72418bcfaec11668")); + Arrays.asList("120270ddf48dfd461f756c89ea1ab074")); executeTest("test Multiple SNP alleles", spec); } @@ -113,7 +113,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{ public void testReverseTrim() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper --contamination_fraction_to_filter 0.05 --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -I " + validationDataLocation + "CEUTrio.HiSeq.b37.chr20.10_11mb.bam -o %s -L 20:10289124 -L 20:10090289", 1, - Arrays.asList("bd867fb341e75a9f1fc78d25bda93f63")); + Arrays.asList("bc5a143868e3ad3acc9bb7c09798cdf2")); executeTest("test reverse trim", spec); } @@ -121,7 +121,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{ public void testMismatchedPLs() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper --contamination_fraction_to_filter 0.05 --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -I " + privateTestDir + "mismatchedPLs.bam -o %s -L 1:24020341", 1, - Arrays.asList("e87419cd42fb9684ee3674ee54abe567")); + Arrays.asList("02fd6357bd1082115822c8a931cbb6a3")); executeTest("test mismatched PLs", spec); } }