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Class name to reflect actual file name. manySampleUGPerformance now operates on 1000 samples! 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5326 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2011-02-26 23:36:04 +00:00
parent b1b9c14c98
commit 146756de79
2 changed files with 38 additions and 44 deletions
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77
scala/qscript/oneoffs/depristo/manySampleUGPerformance.scala
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@ -1,6 +1,6 @@
import org.broadinstitute.sting.queue.QScript
import org.broadinstitute.sting.queue.extensions.gatk._
import org.broadinstitute.sting.queue.extensions.samtools.SamtoolsIndexFunction
import org.broadinstitute.sting.queue.extensions.gatk._
class ManySampleUGPerformanceTesting extends QScript {
@Argument(doc="gatkJarFile", required=false)
@ -9,76 +9,73 @@ class ManySampleUGPerformanceTesting extends QScript {
@Argument(shortName = "R", doc="ref", required=false)
var referenceFile: File = new File("/humgen/1kg/reference/human_g1k_v37.fasta")
val TARGET_INTERVAL = "my.intervals"
val FULL_BAM_LIST = new File("/humgen/1kg/processing/allPopulations_chr20_june_release/allPopulations.june.bam.list")
val MERGED_DIR = new File("/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/manySampleUGPerformance/")
val TARGET_INTERVAL = "my.intervals"
val FULL_BAM_LIST = new File("allPopulations_phase1_release.no_solid.list")
val MERGED_DIR = new File("/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/manySampleUGPerformance/")
trait UNIVERSAL_GATK_ARGS extends CommandLineGATK {
this.logging_level = "INFO";
trait UNIVERSAL_GATK_ARGS extends CommandLineGATK {
this.logging_level = "INFO";
this.jarFile = gatkJarFile;
this.intervals = List(new File(TARGET_INTERVAL));
this.reference_sequence = referenceFile;
this.jobQueue = "gsa";
this.et = Option(org.broadinstitute.sting.gatk.phonehome.GATKRunReport.PhoneHomeOption.STANDARD);
this.dcov = Option(50);
this.reference_sequence = referenceFile;
this.jobQueue = "gsa";
this.memoryLimit = Some(4)
//this.commandDirectory = new File("results");
}
}
def script = {
for (nSamples <- List(1, 2, 5, 10, 50, 100, 200, 300, 400, 500)) {
val sublist = new SliceList(nSamples)
val mergeSublist = new MergeBAMs(sublist.list)
add(sublist)
add(mergeSublist)
add(new Index(mergeSublist.o) )
def script = {
for (nSamples <- 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)
add(sublist)
add(mergeSublist)
add(new Index(mergeSublist.o) )
// SNP calling
add(new Call(sublist.list, nSamples, "dynamic_merge"))
add(new Call(mergeSublist.o, nSamples, "pre_merge"))
//add(new Call(sublist.list, nSamples, "dynamic_merge"))
add(new Call(mergeSublist.o, nSamples, "pre_merge"))
// SNP calling -- no annotations
add(new Call(sublist.list, nSamples, "dynamic_merge_no_annotations") { this.G :+= "None"; })
add(new Call(mergeSublist.o, nSamples, "pre_merge_no_annotations") { this.G :+= "None"; })
//add(new Call(sublist.list, nSamples, "dynamic_merge_no_annotations") { this.G :+= "None"; })
add(new Call(mergeSublist.o, nSamples, "pre_merge_no_annotations") { this.G :+= "none"; })
// CountLoci
add(new MyCountLoci(sublist.list, nSamples, "dynamic_merge"))
//add(new MyCountLoci(sublist.list, nSamples, "dynamic_merge"))
add(new MyCountLoci(mergeSublist.o, nSamples, "pre_merge"))
}
}
}
class Index(bamIn: File) extends SamtoolsIndexFunction {
class Index(bamIn: File) extends SamtoolsIndexFunction {
this.jobQueue = "gsa"
bamFile = bamIn
}
}
class MergeBAMs(bamList: File) extends PrintReads with UNIVERSAL_GATK_ARGS {
class MergeBAMs(bamList: File) extends PrintReads with UNIVERSAL_GATK_ARGS {
this.memoryLimit = Some(3)
this.input_file :+= bamList
this.memoryLimit = Some(16)
this.o = new File(MERGED_DIR + "/" + bamList.getName + ".bam")
}
class Call(@Input(doc="foo") bamList: File, n: Int, name: String) extends UnifiedGenotyper with UNIVERSAL_GATK_ARGS {
class Call(@Input(doc="foo") bamList: File, n: Int, name: String) extends UnifiedGenotyper with UNIVERSAL_GATK_ARGS {
@Output(doc="foo") var outVCF: File = new File("%s.%d.%s.vcf".format(bamList.getName, n, name))
this.memoryLimit = Some(4)
this.input_file :+= bamList
this.jobQueue = "gsa"
this.stand_call_conf = Option(10.0)
this.dcov = Option(50);
this.o = outVCF
}
class MyCountLoci(@Input(doc="foo") bamList: File, n: Int, name: String) extends CountLoci with UNIVERSAL_GATK_ARGS {
@Output(doc="foo") var outFile: File = new File("%s.%d.%s.txt".format(bamList.getName, n, name))
this.memoryLimit = Some(4)
this.input_file :+= bamList
this.jobQueue = "gsa"
this.o = outFile
}
@Output(doc="foo") var outFile: File = new File("%s.%d.%s.txt".format(bamList.getName, n, name))
this.input_file :+= bamList
this.dcov = Option(50);
this.o = outFile
}
class SliceList(n: Int) extends CommandLineFunction {
class SliceList(n: Int) extends CommandLineFunction {
@Output(doc="foo") var list: File = new File("bams.%d.list".format(n))
this.jobQueue = "gsa"
def commandLine = "head -n %d %s > %s".format(n, FULL_BAM_LIST, list)
}
}

5
scala/qscript/oneoffs/depristo/resequencingSamples1KG.scala
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@ -1,10 +1,7 @@
import java.io.File
import org.broadinstitute.sting.commandline.Argument
import org.broadinstitute.sting.queue.QScript
import org.broadinstitute.sting.queue.extensions.gatk._
import org.broadinstitute.sting.queue.extensions.samtools._
class ManySampleUGPerformanceTesting extends QScript {
class resequencingSamples1KG extends QScript {
@Argument(doc="gatkJarFile", required=false)
var gatkJarFile: File = new File("/home/radon01/depristo/dev/GenomeAnalysisTKStable/trunk/dist/GenomeAnalysisTK.jar")