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Now actually checking in the integration test mentioned in the prior commit: compiles the full calling pipeline. 

Removed QScript usages of VariantRecalibrator's -reportDatFile, --report_dat_file


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4668 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kshakir 2010-11-14 04:27:10 +00:00
parent cb1e8ad43a
commit 801c562909
3 changed files with 22 additions and 5 deletions
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1
scala/qscript/fullCallingPipeline.q
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@ -336,7 +336,6 @@ class fullCallingPipeline extends QScript {
recalibrate.rodBind :+= RodBind("input", "VCF", masker.out) recalibrate.rodBind :+= RodBind("input", "VCF", masker.out)
recalibrate.out = swapExt("SnpCalls",masker.out,".vcf",".recalibrated.vcf") recalibrate.out = swapExt("SnpCalls",masker.out,".vcf",".recalibrated.vcf")
recalibrate.target_titv = qscript.target_titv recalibrate.target_titv = qscript.target_titv
recalibrate.report_dat_file = swapExt("SnpCalls/IntermediateFiles", masker.out,".vcf",".recalibrate.dat")
recalibrate.tranches_file = swapExt("SnpCalls/IntermediateFiles", masker.out,".vcf",".recalibrate.tranches") recalibrate.tranches_file = swapExt("SnpCalls/IntermediateFiles", masker.out,".vcf",".recalibrate.tranches")
recalibrate.analysisName = base+"_VariantRecalibrator" recalibrate.analysisName = base+"_VariantRecalibrator"

7
scala/src/org/broadinstitute/sting/queue/pipeline/VariantCalling.scala
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@ -158,7 +158,7 @@ class VariantCalling(yaml: File,gatkJar: File) {
} }
def StandardVariantRecalibrator ( raw_vcf: File, cluster: File, target_titv: scala.Double, out_vcf: File, def StandardVariantRecalibrator ( raw_vcf: File, cluster: File, target_titv: scala.Double, out_vcf: File,
out_tranches: File, out_dat: File) : VariantRecalibrator = { out_tranches: File) : VariantRecalibrator = {
var vr = new VariantRecalibrator with StandardCommandLineGATK var vr = new VariantRecalibrator with StandardCommandLineGATK
vr.analysisName = "VariantQualityRecalibration" vr.analysisName = "VariantQualityRecalibration"
vr.rodBind :+= new RodBind("input","VCF",raw_vcf) vr.rodBind :+= new RodBind("input","VCF",raw_vcf)
@ -166,7 +166,6 @@ class VariantCalling(yaml: File,gatkJar: File) {
vr.target_titv = target_titv vr.target_titv = target_titv
vr.out = out_vcf vr.out = out_vcf
vr.tranches_file = out_tranches vr.tranches_file = out_tranches
vr.report_dat_file = out_dat
vr.tranche :+= "0.1" vr.tranche :+= "0.1"
vr.tranche :+= "1" vr.tranche :+= "1"
vr.tranche :+= "5" vr.tranche :+= "5"
@ -190,7 +189,7 @@ class VariantCalling(yaml: File,gatkJar: File) {
def StandardRecalibrateVariants( snps: File, targetTiTv: scala.Double, recalVcf: File) : List[CommandLineGATK] = { def StandardRecalibrateVariants( snps: File, targetTiTv: scala.Double, recalVcf: File) : List[CommandLineGATK] = {
var clust = StandardVariantCluster(snps, swapExt(snps,".vcf",".cluster")) var clust = StandardVariantCluster(snps, swapExt(snps,".vcf",".cluster"))
var recal = StandardVariantRecalibrator(snps,clust.clusterFile,targetTiTv,swapExt(snps,".vcf",".recal.vcf"), var recal = StandardVariantRecalibrator(snps,clust.clusterFile,targetTiTv,swapExt(snps,".vcf",".recal.vcf"),
swapExt(snps,".vcf",".recal.tranch"),swapExt(snps,".vcf",".recal.dat")) swapExt(snps,".vcf",".recal.tranch"))
var cut = StandardApplyVariantCuts(recal.out,recal.tranches_file,recal.out) var cut = StandardApplyVariantCuts(recal.out,recal.tranches_file,recal.out)
var cmds: List[CommandLineGATK] = Nil var cmds: List[CommandLineGATK] = Nil
@ -337,4 +336,4 @@ class VariantCalling(yaml: File,gatkJar: File) {
def swapExt(file: File, oldExtension: String, newExtension: String) = def swapExt(file: File, oldExtension: String, newExtension: String) =
new File(file.getName.stripSuffix(oldExtension) + newExtension) new File(file.getName.stripSuffix(oldExtension) + newExtension)
} }

19
scala/test/org/broadinstitute/sting/queue/FullCallingPipelineIntegrationTest.scala 100644
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@ -0,0 +1,19 @@
package org.broadinstitute.sting.queue
import org.testng.annotations.Test
import org.broadinstitute.sting.BaseTest
/**
* A temporary integration test to ensure that the full calling pipeline compiles. To be enhanced...
*/
class FullCallingPipelineIntegrationTest extends QScriptTest {
@Test
def testCompileFullCallingPipeline = {
val command = ("-jobProject QueuePipelineTest -S %1$sscala/qscript/fullCallingPipeline.q -Y %2$s " +
"-refseqTable /humgen/gsa-hpprojects/GATK/data/Annotations/refseq/refGene-big-table-hg18.txt " +
"--gatkjar %1$sdist/GenomeAnalysisTK.jar -titv 3.0 -skipCleaning").format(
stingDir, BaseTest.validationDataLocation + "QueuePipelineTestData/QueuePipelineTestData.yaml"
)
executeTest("fullCallingPipeline", command, null)
}
}