diff --git a/scala/qscript/chartl/expanded_targets.q b/scala/qscript/chartl/expanded_targets.q new file mode 100755 index 000000000..ca8de6a00 --- /dev/null +++ b/scala/qscript/chartl/expanded_targets.q @@ -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(_)) + + } +} \ No newline at end of file diff --git a/scala/src/org/broadinstitute/sting/queue/library/ipf/intervals/ExpandIntervals.scala b/scala/src/org/broadinstitute/sting/queue/library/ipf/intervals/ExpandIntervals.scala index ddc85eb59..7526990b8 100755 --- a/scala/src/org/broadinstitute/sting/queue/library/ipf/intervals/ExpandIntervals.scala +++ b/scala/src/org/broadinstitute/sting/queue/library/ipf/intervals/ExpandIntervals.scala @@ -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