From 663184ee9d8560860e9551ca109a72f12c582c7c Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Mon, 12 Dec 2011 18:08:29 -0500
Subject: [PATCH] Added test mode to PPP

* in test mode, no @PG tags are output to the final bam file
* updated pipeline test to use -test mode.
* MD5s updated accordingly
---
 .../sting/queue/qscripts/PacbioProcessingPipeline.scala      | 5 +++++
 .../sting/queue/pipeline/PacbioProcessingPipelineTest.scala  | 3 ++-
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala
index 1d3fb2622..4896eaed3 100755
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala
@@ -47,6 +47,10 @@ class PacbioProcessingPipeline extends QScript {
   @Input(shortName="bwastring", required=false)
   var bwastring: String = ""
 
+  @Hidden
+  @Input(shortName = "test", fullName = "test_mode", required = false)
+  var testMode: Boolean = false
+
   val queueLogDir: String = ".qlog/"
 
   def script = {
@@ -170,6 +174,7 @@ class PacbioProcessingPipeline extends QScript {
     this.input_file :+= inBam
     this.recal_file = inRecalFile
     this.out = outBam
+    this.no_pg_tag = testMode
     this.isIntermediate = false
     this.analysisName = queueLogDir + outBam + ".recalibration"
     this.jobName = queueLogDir + outBam + ".recalibration"
diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/PacbioProcessingPipelineTest.scala b/public/scala/test/org/broadinstitute/sting/queue/pipeline/PacbioProcessingPipelineTest.scala
index b0ac5a6c5..50aa66367 100644
--- a/public/scala/test/org/broadinstitute/sting/queue/pipeline/PacbioProcessingPipelineTest.scala
+++ b/public/scala/test/org/broadinstitute/sting/queue/pipeline/PacbioProcessingPipelineTest.scala
@@ -38,8 +38,9 @@ class PacbioProcessingPipelineTest {
       " -R " + BaseTest.testDir + "exampleFASTA.fasta",
       " -i " + BaseTest.testDir + "exampleBAM.bam",
       " -blasr ",
+      " -test ",
       " -D " + BaseTest.testDir + "exampleDBSNP.vcf").mkString
-    spec.fileMD5s += testOut -> "3a23c96063743ddbc35897331433e205"
+    spec.fileMD5s += testOut -> "f0adce660b55cb91d5f987f9a145471e"
     PipelineTest.executeTest(spec)
   }
 }