From 97e1a5262ed1879e2cb014e92771bab11fff7377 Mon Sep 17 00:00:00 2001 From: chartl Date: Thu, 24 Feb 2011 15:52:04 +0000 Subject: [PATCH] -ct x no longer includes coverage in the previous bin BatchMerge - additional support for indels (can't just test the alternate allele when it's an extended event, must also specify that you want to use the dindel model when you actually test the allele) git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5300 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/walkers/coverage/DepthOfCoverageStats.java | 2 +- .../coverage/DepthOfCoverageB36IntegrationTest.java | 4 ++-- .../coverage/DepthOfCoverageIntegrationTest.java | 12 ++++++------ scala/qscript/playground/BatchMerge.q | 7 +++++++ 4 files changed, 16 insertions(+), 9 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java index faff99f3e..5ad213903 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java @@ -315,7 +315,7 @@ public class DepthOfCoverageStats { public int value2bin(int value) { for ( int index = 0; index < binLeftEndpoints.length; index++ ) { - if ( binLeftEndpoints[index] >= value ) { + if ( binLeftEndpoints[index] > value ) { return index; } } diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageB36IntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageB36IntegrationTest.java index e86a241d5..043b2eaf2 100644 --- a/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageB36IntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageB36IntegrationTest.java @@ -65,9 +65,9 @@ public class DepthOfCoverageB36IntegrationTest extends WalkerTest { spec.addAuxFile("6b15f5330414b6d4e2f6caea42139fa1", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_counts")); spec.addAuxFile("cc6640d82077991dde8a2b523935cdff", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_proportions")); spec.addAuxFile("0fb627234599c258a3fee1b2703e164a", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_statistics")); - spec.addAuxFile("3ad34680c216279c52c7fa0c9e078249", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary")); + spec.addAuxFile("cb73a0fa0cee50f1fb8f249315d38128", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary")); spec.addAuxFile("347b47ef73fbd4e277704ddbd7834f69", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_statistics")); - spec.addAuxFile("65bc90b4839cb9f20e60aba4956f06a9", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary")); + spec.addAuxFile("4ec920335d4b9573f695c39d62748089", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary")); execute("testMapQ0Only",spec); } diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java index 216753be9..59ac1a41e 100644 --- a/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java @@ -59,21 +59,21 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest { spec.addAuxFile("9df5e7e07efeb34926c94a724714c219", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_counts")); spec.addAuxFile("b9a7748e5aec4dc06daed893c901c00d", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_proportions")); spec.addAuxFile("9cd395f47b329b9dd00ad024fcac9929", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_statistics")); - spec.addAuxFile("ca95d2508366d32bf91bf0b0009a023a", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_summary")); + spec.addAuxFile("aec669d64d9dd652dd088a5341835ea5", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_summary")); spec.addAuxFile("f6dbd74d32a48abe71ce08d300bce983", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_statistics")); - spec.addAuxFile("7962a7c09c43ff8b339fa52bce51bfca", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_summary")); + spec.addAuxFile("e3a3467ed259ee3680f8d01980f525b7", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_summary")); spec.addAuxFile("b82846df660f0aac8429aec57c2a62d6", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_cumulative_coverage_counts")); spec.addAuxFile("d32a8c425fadcc4c048bd8b48d0f61e5", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_cumulative_coverage_proportions")); spec.addAuxFile("7b9d0e93bf5b5313995be7010ef1f528", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_statistics")); - spec.addAuxFile("755463d88222c81b84f99615e7b4cfd6", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_summary")); + spec.addAuxFile("2aae346204c5f15517158da8e61a6c16", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_summary")); spec.addAuxFile("e70952f241eebb9b5448f2e7cb288131", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_statistics")); - spec.addAuxFile("51e4c04dfcb4a20c552ca6f013977fa8", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_summary")); + spec.addAuxFile("054ed1e184f46d6a170dc9bf6524270c", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_summary")); spec.addAuxFile("d53431022f7387fe9ac47814ab1fcd88", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_counts")); spec.addAuxFile("650ee3714da7fbad7832c9d4ad49eb51", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_proportions")); spec.addAuxFile("df0ba76e0e6082c0d29fcfd68efc6b77", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_statistics")); - spec.addAuxFile("a52395c883ce8f1a62444d214fe37e88", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary")); + spec.addAuxFile("7dcac2e8962c778081486332a4576dc3", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary")); spec.addAuxFile("a50011571334f17e950ad3ed1149e350", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_statistics")); - spec.addAuxFile("f12a5f97b69718333c4987e3beb98f06", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary")); + spec.addAuxFile("6f3260504295695d765af639539585c9", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary")); execute("testBaseOutputNoFiltering",spec); } diff --git a/scala/qscript/playground/BatchMerge.q b/scala/qscript/playground/BatchMerge.q index 2804e2df0..e0102cd70 100755 --- a/scala/qscript/playground/BatchMerge.q +++ b/scala/qscript/playground/BatchMerge.q @@ -24,6 +24,7 @@ class batchMergePipeline extends QScript { @Hidden @Argument(doc="Min map q",shortName="mmq",required=false) var mmq : Int = 20 @Hidden @Argument(doc="Max mismatching bases",shortName="mmb",required=false) var mmb : Int = 3 @Hidden @Argument(doc="baq gap open penalty, using sets baq to calc when necessary",shortName="baqp",required=false) var baq : Int = -1 + @Hidden @Argument(doc="VCFs are indels",shortName="indel") var indelMode : Boolean = false def script = { @@ -61,6 +62,9 @@ class batchMergePipeline extends QScript { this.scatterCount = 60 this.output_mode = Some(UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_ALL_SITES) this.genotyping_mode = Some(GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES) + if ( batchMerge.indelMode ) { + this.genotype_likelihoods_model = Some(GenotypeLikelihoodsCalculationModel.Model.DINDEL) + } } def newUGCL( bams: (List[File],Int) ) : UGCalcLikelihoods = { @@ -81,6 +85,9 @@ class batchMergePipeline extends QScript { this.memoryLimit = Some(8) this.output_mode = Some(UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_ALL_SITES) this.genotyping_mode = Some(GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES) + if ( batchMerge.indelMode ) { + this.genotype_likelihoods_model = Some(GenotypeLikelihoodsCalculationModel.Model.DINDEL) + } } var cVars : UGCallVariants = new UGCallVariants with CallVariantsArgs