From a3c3d72313e199c722cb5ed0be7895c079547ace Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Mon, 12 Dec 2011 12:35:36 -0500
Subject: [PATCH] Added test mode to DPP

* in test mode, no @PG tags are output to the final bam file
* updated pipeline test to use -test mode.
* MD5s are now dependent on BWA version
---
 .../sting/queue/qscripts/DataProcessingPipeline.scala       | 6 ++++++
 .../sting/queue/pipeline/DataProcessingPipelineTest.scala   | 6 ++++--
 2 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
index ccbe648d6..621afe817 100755
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
@@ -83,6 +83,10 @@ class DataProcessingPipeline extends QScript {
   @Input(doc="Define the default platform for Count Covariates -- useful for techdev purposes only.", fullName="default_platform", shortName="dp", required=false)
   var defaultPlatform: String = ""
 
+  @Hidden
+  @Input(doc="Run the pipeline in test mode only", fullName = "test_mode", shortName = "test", required=false)
+  var testMode: Boolean = false
+
 
   /****************************************************************************
   * Global Variables
@@ -335,6 +339,7 @@ class DataProcessingPipeline extends QScript {
       this.known ++= qscript.indels
     this.consensusDeterminationModel = cleanModelEnum
     this.compress = 0
+    this.noPGTag = qscript.testMode;
     this.scatterCount = nContigs
     this.analysisName = queueLogDir + outBam + ".clean"
     this.jobName = queueLogDir + outBam + ".clean"
@@ -360,6 +365,7 @@ class DataProcessingPipeline extends QScript {
     this.out = outBam
     if (!qscript.intervalString.isEmpty()) this.intervalsString ++= List(qscript.intervalString)
     else if (qscript.intervals != null) this.intervals :+= qscript.intervals
+    this.no_pg_tag = qscript.testMode
     this.scatterCount = nContigs
     this.isIntermediate = false
     this.analysisName = queueLogDir + outBam + ".recalibration"
diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/DataProcessingPipelineTest.scala b/public/scala/test/org/broadinstitute/sting/queue/pipeline/DataProcessingPipelineTest.scala
index 0a5784d51..7e1d09b70 100644
--- a/public/scala/test/org/broadinstitute/sting/queue/pipeline/DataProcessingPipelineTest.scala
+++ b/public/scala/test/org/broadinstitute/sting/queue/pipeline/DataProcessingPipelineTest.scala
@@ -40,8 +40,9 @@ class DataProcessingPipelineTest {
       " -i " + BaseTest.testDir + "exampleBAM.bam",
       " -D " + BaseTest.testDir + "exampleDBSNP.vcf",
       " -nv ",
+      " -test ",
       " -p " + projectName).mkString
-    spec.fileMD5s += testOut -> "a9769a85f15e77505835068353ce4788"
+    spec.fileMD5s += testOut -> "1f85e76de760167a77ed1d9ab4da2936"
     PipelineTest.executeTest(spec)
   }
 
@@ -57,10 +58,11 @@ class DataProcessingPipelineTest {
       " -i " + BaseTest.testDir + "exampleBAM.bam",
       " -D " + BaseTest.testDir + "exampleDBSNP.vcf",
       " -nv ",
+      " -test ",
       " -bwa /home/unix/carneiro/bin/bwa",
       " -bwape ",
       " -p " + projectName).mkString
-    spec.fileMD5s += testOut -> "fad1fd2e69287c1beb423ce17fa464d6"
+    spec.fileMD5s += testOut -> "57416a0abdf9524bc92834d466529708"
     PipelineTest.executeTest(spec)
   }