diff --git a/scala/qscript/oneoffs/depristo/manySampleUGPerformance.scala b/scala/qscript/oneoffs/depristo/manySampleUGPerformance.scala index 1d9bd008c..734db13bd 100755 --- a/scala/qscript/oneoffs/depristo/manySampleUGPerformance.scala +++ b/scala/qscript/oneoffs/depristo/manySampleUGPerformance.scala @@ -21,6 +21,9 @@ class ManySampleUGPerformanceTesting extends QScript { @Argument(shortName = "dcov", doc="dcov", required=false) val DCOV: Int = 50; + @Argument(shortName = "exome", doc="exome ",required=false) + val EXOME_NSAMPLES: Boolean = false; + val MERGED_DIR = new File("/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/manySampleUGPerformance/") trait UNIVERSAL_GATK_ARGS extends CommandLineGATK { @@ -29,13 +32,12 @@ class ManySampleUGPerformanceTesting extends QScript { this.intervals = List(new File(TARGET_INTERVAL)); this.reference_sequence = referenceFile; this.jobQueue = "gsa"; - this.memoryLimit = 4 + this.memoryLimit = 8 //this.commandDirectory = new File("results"); } def script = { - for (nSamples <- List(1, 2, 4, 8, 16, 32, 60)) { -// for (nSamples <- List(1, 2, 5, 10, 50, 100, 200, 300, 400, 500, 600, 700, 800, 900)) { + for (nSamples <- if ( EXOME_NSAMPLES) List(1, 2, 4, 8, 16, 32, 60) else List(1, 2, 5, 10, 50, 100, 200, 300, 400, 500, 600, 700, 800, 900) ) { // for (nSamples <- List(10)) { val sublist = new SliceList(nSamples) val mergeSublist = new MergeBAMs(sublist.list) @@ -52,13 +54,8 @@ class ManySampleUGPerformanceTesting extends QScript { // SNP calling //add(new Call(sublist.list, nSamples, "dynamic_merge")) val gt = new Call(bams, nSamples, name); - gt.exactCalculation = org.broadinstitute.sting.gatk.walkers.genotyper.ExactAFCalculationModel.ExactCalculation.N2_GOLD_STANDARD add(gt) - val gtLinear = new Call(bams, nSamples, name + "_linear"); - gtLinear.exactCalculation = org.broadinstitute.sting.gatk.walkers.genotyper.ExactAFCalculationModel.ExactCalculation.LINEAR_EXPERIMENTAL - add(gtLinear) - // SNP calling -- no annotations //add(new Call(bams.list, nSamples, "dynamic_merge_no_annotations") { this.G :+= "None"; })