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Commit for Khalid 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4876 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-12-18 22:24:18 +00:00
parent 15a33545f4
commit 8118a439c0
2 changed files with 23 additions and 2 deletions
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21
scala/qscript/chartl/expanded_targets.q 100755
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@ -0,0 +1,21 @@
import org.broadinstitute.sting.commandline.ArgumentCollection
import org.broadinstitute.sting.queue.library.ipf.ExpandIntervals
import org.broadinstitute.sting.queue.pipeline.PipelineArgumentCollection
import org.broadinstitute.sting.queue.QScript
class expanded_targets extends QScript {
@ArgumentCollection var args : PipelineArgumentCollection = new PipelineArgumentCollection
@Argument(shortName="bait",doc="The list of baits associated with the target list",required=false) var baitFile : File = _
def script = {
val intervalExpands : List[ExpandIntervals] = (new Range(0,40,1)).toList.map( u => {
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")
})
addAll(intervalExpands)
// intervalExpands.map(_.outList).foreach(makeCalls(_))
}
}

4
scala/src/org/broadinstitute/sting/queue/library/ipf/intervals/ExpandIntervals.scala
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@ -42,11 +42,11 @@ class ExpandIntervals(in : File, start: Int, size: Int, out: File, ref: File, op
val new1 = parser.createGenomeLoc(current.getContig,current.getStart-startInt-sizeInt,current.getStart-startInt)
val new2 = parser.createGenomeLoc(current.getContig,current.getStop+startInt,current.getStop+startInt+sizeInt)
if ( ok(new1) ) {
System.out.println("Printing! %s".format(repr(new1)))
//System.out.println("Printing! %s".format(repr(new1)))
output.print("%s%n".format(repr(new1)))
}
if ( ok(new2) ) {
System.out.println("Printing! %s".format(repr(new2)))
//System.out.println("Printing! %s".format(repr(new2)))
output.print("%s%n".format(repr(new2)))
}
previous = current