From 9f867d77ca746f3063f8c626826bf899dc632e85 Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Thu, 20 Oct 2011 18:44:09 -0400 Subject: [PATCH] no sort order subtle bug fixed. --- .../sting/queue/extensions/picard/SamToFastq.scala | 1 + 1 file changed, 1 insertion(+) diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/SamToFastq.scala b/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/SamToFastq.scala index 2f9f84c63..3a4217e60 100644 --- a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/SamToFastq.scala +++ b/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/SamToFastq.scala @@ -58,6 +58,7 @@ class SamToFastq extends org.broadinstitute.sting.queue.function.JavaCommandLine override def inputBams = input override def outputBam = null + this.sortOrder = null override def commandLine = super.commandLine + " FASTQ=" + fastq +