From 08f0509a5c0fe0d154d88dd71d0a01bb5362d569 Mon Sep 17 00:00:00 2001
From: kshakir <kshakir@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 4 May 2011 12:17:33 +0000
Subject: [PATCH] Disabling the queue/pipeline package by default so that scala
 code can build. If it's not going to be fixed the package should be removed.
 If it is going to be fixed this patch to build.xml should be reverted. Also
 added the old model of indel calling to the FCP.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5749 348d0f76-0448-11de-a6fe-93d51630548a
---
 build.xml                                      | 7 +++++++
 scala/qscript/playground/FullCallingPipeline.q | 1 +
 2 files changed, 8 insertions(+)

diff --git a/build.xml b/build.xml
index 4e7c642ba..e18dfa8de 100644
--- a/build.xml
+++ b/build.xml
@@ -298,6 +298,13 @@
             <src path="${queue-extensions.source.dir}" />
             <include name="**/*.scala"/>
             <exclude name="**/gridengine/**" unless="include.gridengine" />
+            <!--
+            NOTE: Added include.queue.pipeline flag while VQSR v2 is being migrated
+            and the pipeline package is still using the old version.
+            At this moment enabling the flag turns on code that doesn't compile.
+            ASAP determine if package should use v2 or be retired.
+            -->
+            <exclude name="**/queue/pipeline/**" unless="include.queue.pipeline" />
         </scalac>
     </target>
 
diff --git a/scala/qscript/playground/FullCallingPipeline.q b/scala/qscript/playground/FullCallingPipeline.q
index 3f0e460fe..b6a14ce6f 100755
--- a/scala/qscript/playground/FullCallingPipeline.q
+++ b/scala/qscript/playground/FullCallingPipeline.q
@@ -94,6 +94,7 @@ class FullCallingPipeline extends QScript {
     indels.jobOutputFile = ".queue/logs/IndelCalling/UnifiedGenotyper.indels.out"
     indels.downsample_to_coverage = 600
     indels.genotype_likelihoods_model = org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.INDEL
+    indels.GSA_PRODUCTION_ONLY = true /* use old indel genotyper */
     indels.input_file = List(writeBamList.listFile)
     indels.rodBind :+= RodBind("dbsnp", qscript.pipeline.getProject.getGenotypeDbsnpType, qscript.pipeline.getProject.getGenotypeDbsnp)
     indels.out = "IndelCalls/" + base+".indels.vcf"