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Incorporating Khalid's feedback. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5602 348d0f76-0448-11de-a6fe-93d51630548a
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hanna 2011-04-08 16:22:49 +00:00
parent b6e7b5dace
commit 437db28937
1 changed files with 13 additions and 35 deletions
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48
scala/qscript/oneoffs/hanna/PrintReadsAcrossManySamples.q
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@ -1,4 +1,5 @@
import java.io.PrintWriter
import org.broadinstitute.sting.queue.function.ListWriterFunction
import org.broadinstitute.sting.queue.QScript
import org.broadinstitute.sting.queue.extensions.gatk._
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException
@ -9,12 +10,6 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException
* Future syntax will simplify running the GATK so please expect the syntax below to change significantly.
*/
class PrintReadsAcrossManySamples extends QScript {
// The full packaged jar should be used.
// You can build this jar via 'ant package' and then find it under
// 'Sting/dist/packages/GenomeAnalysisTK-*/GenomeAnalysisTK.jar'
@Input(doc="The path to the packaged GenomeAnalysisTK.jar file.", shortName="gatk")
var gatkJar: File = null
@Input(doc="The reference file for the bam files.", shortName="R")
var referenceFile: File = null
@ -25,7 +20,7 @@ class PrintReadsAcrossManySamples extends QScript {
// Set[T] = Set.empty[T]
// Option[T] = None
@Input(doc="One or more bam files.", shortName="I")
var bamFiles: List[File] = Nil
var bamFile: File = _
@Input(doc="Name of the test case", fullName="test_case",required=false)
var testCaseName: String = "."
@ -36,43 +31,26 @@ class PrintReadsAcrossManySamples extends QScript {
@Input(doc="Step size",fullName="step_size",required=false)
var stepSize = 1
// This trait allows us set the variables below in one place,
// and then reuse this trait on each CommandLineGATK function below.
trait PrintReadsAcrossManySamplesArguments extends CommandLineGATK {
this.jarFile = PrintReadsAcrossManySamples.this.gatkJar
this.reference_sequence = PrintReadsAcrossManySamples.this.referenceFile
this.memoryLimit = 8
}
def script = {
if(bamFiles.size != 1)
throw new ReviewedStingException("-I argument must consist of exactly one file containing a list of BAM files.");
var lines = scala.io.Source.fromFile(bamFile).getLines.map(new File(_)).toList
var lines: List[String] = List[String]()
for(line <- scala.io.Source.fromFile(bamFiles(0)).getLines) {
lines = lines ::: List(line)
}
for(numBams <- 1 to (maxBams min lines.size) by stepSize) {
val basePath = "%s/%03d_bams".format(testCaseName,numBams)
for(numBams <- 1 to math.min(maxBams,lines.size) by stepSize) {
val dir = new File(testCaseName + "/%03d_bams".format(numBams))
dir.mkdir()
val file = new File(dir,"bams.list")
val writer = new PrintWriter(file)
for(bamIndex <- 0 to numBams-1)
writer.println(lines(bamIndex))
writer.close()
val writeBamList = new ListWriterFunction
writeBamList.inputFiles = lines.take(numBams)
writeBamList.listFile = new File(basePath+"/bams.list")
add(writeBamList)
// Create the function that we can run.
val printreads = new PrintReads with PrintReadsAcrossManySamplesArguments
val printreads = new PrintReads
printreads.jobOutputFile = new File(dir, "PrintReads.out")
printreads.input_file = List(file)
printreads.jobOutputFile = new File(basePath+"/PrintReads.out")
printreads.input_file = List(writeBamList.listFile)
printreads.reference_sequence = referenceFile
printreads.out = new File("/dev/null")
printreads.memoryLimit = 8
add(printreads)
}