From 58d45393048c6cdd429bfbb3bd58d96ca66d5caf Mon Sep 17 00:00:00 2001 From: Guillermo del Angel Date: Wed, 4 Jan 2012 15:28:26 -0500 Subject: [PATCH] Enabled banded indel computation by default. Reversed logic in input UG argument so that we can still disable it if required. Minor changes to integration tests due to minor differences in GL's and in annotations --- .../IndelGenotypeLikelihoodsCalculationModel.java | 2 +- .../gatk/walkers/genotyper/UnifiedArgumentCollection.java | 6 +++--- .../genotyper/UnifiedGenotyperIntegrationTest.java | 8 ++++---- 3 files changed, 8 insertions(+), 8 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java index fe2086d47..8d279005b 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java @@ -81,7 +81,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood protected IndelGenotypeLikelihoodsCalculationModel(UnifiedArgumentCollection UAC, Logger logger) { super(UAC, logger); pairModel = new PairHMMIndelErrorModel(UAC.INDEL_GAP_OPEN_PENALTY,UAC.INDEL_GAP_CONTINUATION_PENALTY, - UAC.OUTPUT_DEBUG_INDEL_INFO, UAC.BANDED_INDEL_COMPUTATION); + UAC.OUTPUT_DEBUG_INDEL_INFO, !UAC.DONT_DO_BANDED_INDEL_COMPUTATION); alleleList = new ArrayList(); getAlleleListFromVCF = UAC.GenotypingMode == GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES; minIndelCountForGenotyping = UAC.MIN_INDEL_COUNT_FOR_GENOTYPING; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java index 5713432b4..4639d67a7 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java @@ -146,8 +146,8 @@ public class UnifiedArgumentCollection { public int INDEL_HAPLOTYPE_SIZE = 80; @Hidden - @Argument(fullName = "bandedIndel", shortName = "bandedIndel", doc = "Banded Indel likelihood computation", required = false) - public boolean BANDED_INDEL_COMPUTATION = false; + @Argument(fullName = "noBandedIndel", shortName = "noBandedIndel", doc = "Don't do Banded Indel likelihood computation", required = false) + public boolean DONT_DO_BANDED_INDEL_COMPUTATION = false; @Hidden @Argument(fullName = "indelDebug", shortName = "indelDebug", doc = "Output indel debug info", required = false) @@ -184,7 +184,7 @@ public class UnifiedArgumentCollection { // todo- arguments to remove uac.IGNORE_SNP_ALLELES = IGNORE_SNP_ALLELES; - uac.BANDED_INDEL_COMPUTATION = BANDED_INDEL_COMPUTATION; + uac.DONT_DO_BANDED_INDEL_COMPUTATION = DONT_DO_BANDED_INDEL_COMPUTATION; uac.MULTI_ALLELIC = MULTI_ALLELIC; return uac; } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java index 7c0dba558..a91ea1c87 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java @@ -265,7 +265,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1, - Arrays.asList("fa4f3ee67d98b64102a8a3ec81a3bc81")); + Arrays.asList("c60a44ba94a80a0cb1fba8b6f90a13cd")); executeTest("test MultiSample Pilot2 indels with alleles passed in", spec1); } @@ -275,7 +275,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1, - Arrays.asList("df90890e43d735573a3b3e4f289ca46b")); + Arrays.asList("36ce53ae4319718ad9c8ae391deebc8c")); executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec2); } @@ -285,7 +285,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec( baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "ALL.wgs.union_v2.20101123.indels.sites.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,080,000", 1, - Arrays.asList("cff6dd0f4eb1ef0b6fc476da6ffead19")); + Arrays.asList("d356cbaf240d7025d1aecdabaff3a3e0")); executeTest("test MultiSample Pilot2 indels with complicated records", spec3); } @@ -294,7 +294,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec4 = new WalkerTest.WalkerTestSpec( baseCommandIndelsb37 + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "ALL.wgs.union_v2_chr20_100_110K.20101123.indels.sites.vcf -I " + validationDataLocation + "phase1_GBR_realigned.chr20.100K-110K.bam -o %s -L 20:100,000-110,000", 1, - Arrays.asList("1e2a4aab26e9ab0dae709d33a669e036")); + Arrays.asList("947c12ef2a8c29ae787cd11be8c565c8")); executeTest("test MultiSample Phase1 indels with complicated records", spec4); }