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-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
This commit is contained in:
chartl 2011-02-24 15:52:04 +00:00
parent ee6f112556
commit 97e1a5262e
4 changed files with 16 additions and 9 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java
View File

@ -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;
}
}

4
java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageB36IntegrationTest.java
View File

@ -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);
}

12
java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java
View File

@ -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);
}

7
scala/qscript/playground/BatchMerge.q
View File

@ -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