From bc4305c956739516b4aa413698c5a0a80a3f3b25 Mon Sep 17 00:00:00 2001
From: fromer <fromer@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 23 May 2011 21:11:44 +0000
Subject: [PATCH] Added memory limit parameter

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5855 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../oneoffs/fromer/ScatteredFullVariantAnnotator.scala        | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/scala/qscript/oneoffs/fromer/ScatteredFullVariantAnnotator.scala b/scala/qscript/oneoffs/fromer/ScatteredFullVariantAnnotator.scala
index 27797f604..1be4c3cf1 100644
--- a/scala/qscript/oneoffs/fromer/ScatteredFullVariantAnnotator.scala
+++ b/scala/qscript/oneoffs/fromer/ScatteredFullVariantAnnotator.scala
@@ -28,6 +28,8 @@ class ScatteredFullVariantAnnotator extends QScript {
   @Output(doc = "annotated file to output", shortName = "o", required = true)
   var outputAnnotated: File = _
 
+  @Output(doc = "Memory limit", fullName = "memoryLimit", shortName = "m", required = false)
+  var memoryLimit = 3
 
   def script = {
     add(new ScatteredFullVariantAnnotator())
@@ -38,6 +40,8 @@ class ScatteredFullVariantAnnotator extends QScript {
     this.jarFile = qscript.gatkJarFile
     this.reference_sequence = qscript.referenceFile
     this.input_file = List(qscript.bams)
+
+    this.memoryLimit = qscript.memoryLimit
     this.logging_level = "INFO"
 
     this.rodToIntervalTrackName = "variant"