From 801c56290962ec287eda2c6f43754b754eedcdbe Mon Sep 17 00:00:00 2001
From: kshakir <kshakir@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sun, 14 Nov 2010 04:27:10 +0000
Subject: [PATCH] Now actually checking in the integration test mentioned in
 the prior commit: compiles the full calling pipeline. Removed QScript usages
 of VariantRecalibrator's -reportDatFile, --report_dat_file

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4668 348d0f76-0448-11de-a6fe-93d51630548a
---
 scala/qscript/fullCallingPipeline.q           |  1 -
 .../sting/queue/pipeline/VariantCalling.scala |  7 +++----
 .../FullCallingPipelineIntegrationTest.scala  | 19 +++++++++++++++++++
 3 files changed, 22 insertions(+), 5 deletions(-)
 create mode 100644 scala/test/org/broadinstitute/sting/queue/FullCallingPipelineIntegrationTest.scala

diff --git a/scala/qscript/fullCallingPipeline.q b/scala/qscript/fullCallingPipeline.q
index ca907f997..a49ac1096 100755
--- a/scala/qscript/fullCallingPipeline.q
+++ b/scala/qscript/fullCallingPipeline.q
@@ -336,7 +336,6 @@ class fullCallingPipeline extends QScript {
     recalibrate.rodBind :+= RodBind("input", "VCF", masker.out)
     recalibrate.out = swapExt("SnpCalls",masker.out,".vcf",".recalibrated.vcf")
     recalibrate.target_titv = qscript.target_titv
-    recalibrate.report_dat_file = swapExt("SnpCalls/IntermediateFiles", masker.out,".vcf",".recalibrate.dat")
     recalibrate.tranches_file = swapExt("SnpCalls/IntermediateFiles", masker.out,".vcf",".recalibrate.tranches")
     recalibrate.analysisName = base+"_VariantRecalibrator"
 
diff --git a/scala/src/org/broadinstitute/sting/queue/pipeline/VariantCalling.scala b/scala/src/org/broadinstitute/sting/queue/pipeline/VariantCalling.scala
index 36f7cd537..e7991010d 100755
--- a/scala/src/org/broadinstitute/sting/queue/pipeline/VariantCalling.scala
+++ b/scala/src/org/broadinstitute/sting/queue/pipeline/VariantCalling.scala
@@ -158,7 +158,7 @@ class VariantCalling(yaml: File,gatkJar: File) {
   }
 
   def StandardVariantRecalibrator ( raw_vcf: File, cluster: File, target_titv: scala.Double, out_vcf: File,
-                                              out_tranches: File, out_dat: File) : VariantRecalibrator = {
+                                              out_tranches: File) : VariantRecalibrator = {
     var vr = new VariantRecalibrator with StandardCommandLineGATK
     vr.analysisName = "VariantQualityRecalibration"
     vr.rodBind :+= new RodBind("input","VCF",raw_vcf)
@@ -166,7 +166,6 @@ class VariantCalling(yaml: File,gatkJar: File) {
     vr.target_titv = target_titv
     vr.out = out_vcf
     vr.tranches_file = out_tranches
-    vr.report_dat_file = out_dat
     vr.tranche :+= "0.1"
     vr.tranche :+= "1"
     vr.tranche :+= "5"
@@ -190,7 +189,7 @@ class VariantCalling(yaml: File,gatkJar: File) {
   def StandardRecalibrateVariants( snps: File, targetTiTv: scala.Double, recalVcf: File) : List[CommandLineGATK] = {
     var clust = StandardVariantCluster(snps, swapExt(snps,".vcf",".cluster"))
     var recal = StandardVariantRecalibrator(snps,clust.clusterFile,targetTiTv,swapExt(snps,".vcf",".recal.vcf"),
-                swapExt(snps,".vcf",".recal.tranch"),swapExt(snps,".vcf",".recal.dat"))
+                swapExt(snps,".vcf",".recal.tranch"))
     var cut = StandardApplyVariantCuts(recal.out,recal.tranches_file,recal.out)
 
     var cmds: List[CommandLineGATK] = Nil
@@ -337,4 +336,4 @@ class VariantCalling(yaml: File,gatkJar: File) {
   def swapExt(file: File, oldExtension: String, newExtension: String) =
     new File(file.getName.stripSuffix(oldExtension) + newExtension)
 
-}
\ No newline at end of file
+}
diff --git a/scala/test/org/broadinstitute/sting/queue/FullCallingPipelineIntegrationTest.scala b/scala/test/org/broadinstitute/sting/queue/FullCallingPipelineIntegrationTest.scala
new file mode 100644
index 000000000..0c5f5bace
--- /dev/null
+++ b/scala/test/org/broadinstitute/sting/queue/FullCallingPipelineIntegrationTest.scala
@@ -0,0 +1,19 @@
+package org.broadinstitute.sting.queue
+
+import org.testng.annotations.Test
+import org.broadinstitute.sting.BaseTest
+
+/**
+ * A temporary integration test to ensure that the full calling pipeline compiles.  To be enhanced...
+ */
+class FullCallingPipelineIntegrationTest extends QScriptTest {
+  @Test
+  def testCompileFullCallingPipeline = {
+    val command = ("-jobProject QueuePipelineTest -S %1$sscala/qscript/fullCallingPipeline.q -Y %2$s " +
+            "-refseqTable /humgen/gsa-hpprojects/GATK/data/Annotations/refseq/refGene-big-table-hg18.txt " +
+            "--gatkjar %1$sdist/GenomeAnalysisTK.jar -titv 3.0 -skipCleaning").format(
+              stingDir, BaseTest.validationDataLocation + "QueuePipelineTestData/QueuePipelineTestData.yaml"
+              )
+    executeTest("fullCallingPipeline", command, null)
+  }
+}