21 lines
914 B
Plaintext
Executable File
21 lines
914 B
Plaintext
Executable File
import org.broadinstitute.sting.commandline.ArgumentCollection
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import org.broadinstitute.sting.queue.library.ipf.ExpandIntervals
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import org.broadinstitute.sting.queue.pipeline.PipelineArgumentCollection
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import org.broadinstitute.sting.queue.QScript
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class expanded_targets extends QScript {
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@ArgumentCollection var args : PipelineArgumentCollection = new PipelineArgumentCollection
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@Argument(shortName="bait",doc="The list of baits associated with the target list",required=false) var baitFile : File = _
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def script = {
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val intervalExpands : List[ExpandIntervals] = (new Range(0,40,1)).toList.map( u => {
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new ExpandIntervals(args.projectIntervals,1+5*u,5,new File(System.getProperty("user.dir")+"/"+args.projectName+"_expanded_%d_%d.interval_list".format(1+5*u,6+5*u)),args.projectRef,"BED")
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})
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addAll(intervalExpands)
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// intervalExpands.map(_.outList).foreach(makeCalls(_))
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}
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} |