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Since Picard's FixMateInformation merges, fixes mates, and sorts, allow it to be used as a gather function. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3891 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-07-28 15:09:19 +00:00
parent e1a34685fd
commit cd9395fa14
1 changed files with 17 additions and 0 deletions
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17
scala/src/org/broadinstitute/sting/queue/function/scattergather/FixMatesGatherFunction.scala 100644
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package org.broadinstitute.sting.queue.function.scattergather
import java.io.File
import org.broadinstitute.sting.commandline.Input
class BamGatherFunction extends GatherFunction {
type GatherType = File
@Input(doc="Picard FixMateInformation.jar. At the Broad this can be found at /seq/software/picard/current/bin/FixMateInformation.jar. Outside the broad see http://picard.sourceforge.net/")
var picardFixMatesJar: String = _
@Input(doc="Compression level 1-9", required=false)
var picardMergeCompressionLevel: Option[Int] = None
def commandLine = "java -Djava.io.tmpdir=/broad/shptmp/queue -jar %s%s%s%s".format(picardFixMatesJar,
optional(" COMPRESSION_LEVEL=", picardMergeCompressionLevel), " VALIDATION_STRINGENCY=SILENT SO=coordinate OUTPUT=" + originalOutput, repeat(" INPUT=", gatherParts))
}