60 lines
2.0 KiB
Plaintext
60 lines
2.0 KiB
Plaintext
import java.io.PrintWriter
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import org.broadinstitute.sting.queue.function.ListWriterFunction
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import org.broadinstitute.sting.queue.QScript
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import org.broadinstitute.sting.queue.extensions.gatk._
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import org.broadinstitute.sting.utils.exceptions.ReviewedStingException
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/**
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* A pipeline for Queue that runs a custom walker outside of the GATK jar.
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* NOTE: This code is an unsupported example for soliciting feedback on how to improve Queue.
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* Future syntax will simplify running the GATK so please expect the syntax below to change significantly.
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*/
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class PrintReadsAcrossManySamples extends QScript {
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@Input(doc="The reference file for the bam files.", shortName="R")
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var referenceFile: File = null
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// NOTE: Do not initialize List, Set, or Option to null
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// as you won't be able to update the collection.
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// By default set:
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// List[T] = Nil
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// Set[T] = Set.empty[T]
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// Option[T] = None
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@Input(doc="One or more bam files.", shortName="I")
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var bamFile: File = _
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@Input(doc="Name of the test case", fullName="test_case",required=false)
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var testCaseName: String = "."
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@Input(doc="Max number of bam files to process", fullName="max_bams",required=false)
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var maxBams = 1
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@Input(doc="Step size",fullName="step_size",required=false)
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var stepSize = 1
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def script = {
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var lines = scala.io.Source.fromFile(bamFile).getLines.map(new File(_)).toList
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for(numBams <- 1 to (maxBams min lines.size) by stepSize) {
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val basePath = "%s/%03d_bams".format(testCaseName,numBams)
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val writeBamList = new ListWriterFunction
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writeBamList.inputFiles = lines.take(numBams)
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writeBamList.listFile = new File(basePath+"/bams.list")
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add(writeBamList)
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// Create the function that we can run.
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val printreads = new PrintReads
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printreads.jobOutputFile = new File(basePath+"/PrintReads.out")
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printreads.input_file = List(writeBamList.listFile)
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printreads.reference_sequence = referenceFile
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printreads.out = new File("/dev/null")
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printreads.memoryLimit = 8
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add(printreads)
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}
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}
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}
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