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Better merge command 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3797 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2010-07-15 17:02:47 +00:00
parent dfddf8fd75
commit 6bf5df4eb5
1 changed files with 1 additions and 1 deletions
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2
scala/src/org/broadinstitute/sting/queue/function/scattergather/BamGatherFunction.scala
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@ -13,5 +13,5 @@ class BamGatherFunction extends GatherFunction {
var picardMergeCompressionLevel: Option[Int] = None var picardMergeCompressionLevel: Option[Int] = None
def commandLine = "java -jar %s%s%s%s".format(picardMergeSamFilesJar, def commandLine = "java -jar %s%s%s%s".format(picardMergeSamFilesJar,
optional(" COMPRESSION_LEVEL=", picardMergeCompressionLevel), " OUTPUT=" + originalOutput, repeat(" INPUT=", gatherParts)) optional(" COMPRESSION_LEVEL=", picardMergeCompressionLevel), " AS=true VALIDATION_STRINGENCY=SILENT SO=coordinate OUTPUT=" + originalOutput, repeat(" INPUT=", gatherParts))
} }