From 6bf5df4eb5f880928d4336bd9e1682e1923adc50 Mon Sep 17 00:00:00 2001 From: depristo Date: Thu, 15 Jul 2010 17:02:47 +0000 Subject: [PATCH] Better merge command git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3797 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/queue/function/scattergather/BamGatherFunction.scala | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scala/src/org/broadinstitute/sting/queue/function/scattergather/BamGatherFunction.scala b/scala/src/org/broadinstitute/sting/queue/function/scattergather/BamGatherFunction.scala index 4c443a02a..b433ee10e 100644 --- a/scala/src/org/broadinstitute/sting/queue/function/scattergather/BamGatherFunction.scala +++ b/scala/src/org/broadinstitute/sting/queue/function/scattergather/BamGatherFunction.scala @@ -13,5 +13,5 @@ class BamGatherFunction extends GatherFunction { var picardMergeCompressionLevel: Option[Int] = None 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)) }