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Bringing script up to date 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5526 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2011-03-27 20:49:07 +00:00
parent cd8321cdc9
commit cdb0bde952
1 changed files with 5 additions and 8 deletions
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13
scala/qscript/oneoffs/depristo/manySampleUGPerformance.scala
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@ -21,6 +21,9 @@ class ManySampleUGPerformanceTesting extends QScript {
@Argument(shortName = "dcov", doc="dcov", required=false) @Argument(shortName = "dcov", doc="dcov", required=false)
val DCOV: Int = 50; 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/") val MERGED_DIR = new File("/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/manySampleUGPerformance/")
trait UNIVERSAL_GATK_ARGS extends CommandLineGATK { trait UNIVERSAL_GATK_ARGS extends CommandLineGATK {
@ -29,13 +32,12 @@ class ManySampleUGPerformanceTesting extends QScript {
this.intervals = List(new File(TARGET_INTERVAL)); this.intervals = List(new File(TARGET_INTERVAL));
this.reference_sequence = referenceFile; this.reference_sequence = referenceFile;
this.jobQueue = "gsa"; this.jobQueue = "gsa";
this.memoryLimit = 4 this.memoryLimit = 8
//this.commandDirectory = new File("results"); //this.commandDirectory = new File("results");
} }
def script = { def script = {
for (nSamples <- List(1, 2, 4, 8, 16, 32, 60)) { 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(1, 2, 5, 10, 50, 100, 200, 300, 400, 500, 600, 700, 800, 900)) {
// for (nSamples <- List(10)) { // for (nSamples <- List(10)) {
val sublist = new SliceList(nSamples) val sublist = new SliceList(nSamples)
val mergeSublist = new MergeBAMs(sublist.list) val mergeSublist = new MergeBAMs(sublist.list)
@ -52,13 +54,8 @@ class ManySampleUGPerformanceTesting extends QScript {
// SNP calling // SNP calling
//add(new Call(sublist.list, nSamples, "dynamic_merge")) //add(new Call(sublist.list, nSamples, "dynamic_merge"))
val gt = new Call(bams, nSamples, name); val gt = new Call(bams, nSamples, name);
gt.exactCalculation = org.broadinstitute.sting.gatk.walkers.genotyper.ExactAFCalculationModel.ExactCalculation.N2_GOLD_STANDARD
add(gt) 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 // SNP calling -- no annotations
//add(new Call(bams.list, nSamples, "dynamic_merge_no_annotations") { this.G :+= "None"; }) //add(new Call(bams.list, nSamples, "dynamic_merge_no_annotations") { this.G :+= "None"; })