From 68a2f1243d245533df45ae8ade143b46860e6e33 Mon Sep 17 00:00:00 2001 From: Laura Gauthier Date: Thu, 11 Jun 2015 10:52:23 -0400 Subject: [PATCH] Finished draft of code for new map-combine-reduce annotation framework All VQSR annotations can be generated in allele-specific mode Pull out allele-specific annotations in AS_Standard annotation group --- .../haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java | 2 +- .../walkers/variantutils/CombineGVCFsIntegrationTest.java | 2 +- .../walkers/variantutils/GenotypeGVCFsIntegrationTest.java | 4 ++-- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java index 1bbba4e28..d13905cfb 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java @@ -316,7 +316,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest { public void testAlleleSpecificAnnotations() { final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -G Standard -G AS_Standard --disableDithering", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam", "20:10433000-10437000", GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER); - final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("9a2887ed7afa829a75ec7d6e11dfc45f")); + final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("fc10e56ffa5e230c1a1c8bdf9673bdaa")); spec.disableShadowBCF(); executeTest(" testAlleleSpecificAnnotations", spec); } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFsIntegrationTest.java index 75d557949..080c8da02 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFsIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFsIntegrationTest.java @@ -277,7 +277,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest { public void testAlleleSpecificAnnotations() throws Exception { final String cmd = "-T CombineGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard -V " + privateTestDir + "NA12878.AS.chr20snippet.g.vcf -V " + privateTestDir + "NA12891.AS.chr20snippet.g.vcf"; - final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("f06d60332cd46036813f652de6d807c9")); + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("cbb2571eeb95e661acee8f9e1d1cbfbd")); spec.disableShadowBCF(); executeTest("testAlleleSpecificAnnotations", spec); } 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 e75e0a109..1909060a0 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 @@ -565,7 +565,7 @@ 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, Arrays.asList("69b5d245a7411ab45e6bd211cc09a53d")); + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("f62ae282ec8e32f6104ef84237b8a5a4")); spec.disableShadowBCF(); executeTest("testAlleleSpecificAnnotations", spec); } @@ -575,7 +575,7 @@ 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, Arrays.asList("14ecc30b631afce3e3029484c9ee7b92")); + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("1eefb0ed407b9071f09f9189c9ad45cf")); spec.disableShadowBCF(); executeTest("testAlleleSpecificAnnotations", spec); }