From a3f31e5df0af91449e9931be6cdf4dd4c4d589d2 Mon Sep 17 00:00:00 2001 From: kshakir Date: Fri, 17 Sep 2010 18:22:07 +0000 Subject: [PATCH] When QScript writers use the RodBind, then the File version of the same argument should be optional, i.e. should not always try to output the file, which when unpopulated will be null. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4305 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/queue/extensions/gatk/RodBindField.java | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/java/src/org/broadinstitute/sting/queue/extensions/gatk/RodBindField.java b/java/src/org/broadinstitute/sting/queue/extensions/gatk/RodBindField.java index b98b2aa91..ea180d33c 100644 --- a/java/src/org/broadinstitute/sting/queue/extensions/gatk/RodBindField.java +++ b/java/src/org/broadinstitute/sting/queue/extensions/gatk/RodBindField.java @@ -64,9 +64,13 @@ public class RodBindField extends ArgumentField { @Override protected boolean isRequired() { return this.isRequired; } @Override public String getCommandLineAddition() { + // TODO: Stop allowing the generic "rodBind" triplets to satisfy the requirement after @Requires are fixed. + return String.format(" + optional(\" -B:%s,%s \", %s)", + /* return String.format(this.useOption() ? " + optional(\" -B:%s,%s \", %s)" : " + \" -B:%s,%s \" + %s", + */ this.trackName, this.typeName, getFieldName()); }