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Put a band-aid on the FCP by switching use of DINDEL to INDEL and explicitly running UG the old way with just indels and just snps. 

Switched YAML parser to new Broad parser which will additionally update picard cleaned bams to the latest version if the project and sample are specified.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5634 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kshakir 2011-04-14 02:22:31 +00:00
parent 2089c3bdef
commit 475ad1259d
2 changed files with 6 additions and 5 deletions
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9
scala/qscript/playground/FullCallingPipeline.q
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@ -8,7 +8,7 @@ import org.broadinstitute.sting.queue.function.scattergather.{GatherFunction, Cl
import org.broadinstitute.sting.queue.library.ipf.intervals.ExpandIntervals import org.broadinstitute.sting.queue.library.ipf.intervals.ExpandIntervals
import org.broadinstitute.sting.queue.QScript import org.broadinstitute.sting.queue.QScript
import collection.JavaConversions._ import collection.JavaConversions._
import org.broadinstitute.sting.utils.yaml.YamlUtils import org.broadinstitute.sting.utils.broad.PicardPipeline
class FullCallingPipeline extends QScript { class FullCallingPipeline extends QScript {
qscript => qscript =>
@ -49,8 +49,8 @@ class FullCallingPipeline extends QScript {
// ------------ SETUP THE PIPELINE ----------- // // ------------ SETUP THE PIPELINE ----------- //
def script = { def script() {
pipeline = YamlUtils.load(classOf[Pipeline], qscript.yamlFile) pipeline = PicardPipeline.parse(qscript.yamlFile)
val projectBase: String = qscript.pipeline.getProject.getName val projectBase: String = qscript.pipeline.getProject.getName
@ -175,7 +175,7 @@ class FullCallingPipeline extends QScript {
indels.jobOutputFile = new File(".queue/logs/IndelCalling/UnifiedGenotyper.indels.out") indels.jobOutputFile = new File(".queue/logs/IndelCalling/UnifiedGenotyper.indels.out")
indels.memoryLimit = 6 indels.memoryLimit = 6
indels.downsample_to_coverage = 600 indels.downsample_to_coverage = 600
indels.genotype_likelihoods_model = org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.DINDEL indels.genotype_likelihoods_model = org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.INDEL
indels.input_file = bamFiles indels.input_file = bamFiles
indels.rodBind :+= RodBind("dbsnp", qscript.pipeline.getProject.getGenotypeDbsnpType, qscript.pipeline.getProject.getGenotypeDbsnp) indels.rodBind :+= RodBind("dbsnp", qscript.pipeline.getProject.getGenotypeDbsnpType, qscript.pipeline.getProject.getGenotypeDbsnp)
indels.out = new File("IndelCalls", base+".indels.vcf") indels.out = new File("IndelCalls", base+".indels.vcf")
@ -213,6 +213,7 @@ class FullCallingPipeline extends QScript {
snps.memoryLimit = 6 snps.memoryLimit = 6
snps.downsample_to_coverage = 600 snps.downsample_to_coverage = 600
snps.input_file = bamFiles snps.input_file = bamFiles
snps.genotype_likelihoods_model = org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.SNP
snps.rodBind :+= RodBind("dbsnp", qscript.pipeline.getProject.getGenotypeDbsnpType, qscript.pipeline.getProject.getGenotypeDbsnp) snps.rodBind :+= RodBind("dbsnp", qscript.pipeline.getProject.getGenotypeDbsnpType, qscript.pipeline.getProject.getGenotypeDbsnp)
snps.out = new File("SnpCalls", base+".snps.vcf") snps.out = new File("SnpCalls", base+".snps.vcf")

2
scala/test/org/broadinstitute/sting/queue/pipeline/playground/MultiFullCallingPipelineTest.scala
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@ -54,7 +54,7 @@ class MultiFullCallingPipelineTest {
final def convertDatasets: Array[Array[AnyRef]] = final def convertDatasets: Array[Array[AnyRef]] =
datasets.map(dataset => Array(dataset.asInstanceOf[AnyRef])).toArray datasets.map(dataset => Array(dataset.asInstanceOf[AnyRef])).toArray
@Test(dataProvider="datasets", enabled=false) @Test(dataProvider="datasets")
def testMultiFullCallingPipeline(dataset: MultiPipelineDataset) { def testMultiFullCallingPipeline(dataset: MultiPipelineDataset) {
val projectName = dataset.name val projectName = dataset.name
val testName = "MultiFullCallingPipeline-" + projectName val testName = "MultiFullCallingPipeline-" + projectName