A successful attempt at a queue integration test, ensuring that the InProcessFunction libraries are working as expected.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5190 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-03 21:30:35 +00:00 · 2011-02-03 21:30:35 +00:00 · bfc6ef1753
parent 358a400474
commit bfc6ef1753
1 changed files with 72 additions and 0 deletions
--- a/scala/test/org/broadinstitute/sting/queue/pipeline/IPFLibraryTest.scala
+++ b/scala/test/org/broadinstitute/sting/queue/pipeline/IPFLibraryTest.scala
@ -0,0 +1,72 @@
+package org.broadinstitute.sting.queue.pipeline
+
+import org.testng.annotations.Test
+import org.broadinstitute.sting.queue.pipeline.{PipelineTest, PipelineTestSpec}
+import org.broadinstitute.sting.BaseTest
+
+class IPFLibraryTest {
+
+  @Test
+  def testVCFExtractSites {
+    var testOut = "vcfes.vcf"
+    val spec = new PipelineTestSpec
+    spec.name = "vcfExtractSites"
+    spec.args = "-S scala/qscript/oneoffs/QTools.q -T VCFExtractSites -ivcf %s -out %s".format(
+      BaseTest.validationDataLocation + "omni_1212.subset.b37.vcf", testOut
+    )
+    spec.fileMD5s += testOut -> "4f496b8cf90302428a9edda486a337f4"
+    PipelineTest.executeTest(spec)
+  }
+
+  @Test
+  def testVCFExtractSamples {
+    var testOut = "vcf.extract.samples.vcf"
+    val spec = new PipelineTestSpec
+    spec.name = "vcfExtractSamples"
+    spec.args = "-S scala/qscript/oneoffs/QTools.q -T VCFExtractSamples -ivcf %s -out %s -sm HG00107,HG00500,NA18501,NA18942".format(
+      BaseTest.validationDataLocation + "omni_1212.subset.b37.vcf", testOut
+    )
+
+    spec.fileMD5s += testOut -> "180d5a2e7a1fbc5117de6705bde3a7c8"
+  }
+
+  @Test
+  def testVCFExtractIntervals {
+    var testOut = "vcf.extract.intervals.list"
+    val spec = new PipelineTestSpec
+    spec.name = "vcfExtractIntervals"
+    spec.args = "-S scala/qscript/oneoffs/QTools.q -T VCFExtractIntervals -ivcf %s -out %s".format(
+      BaseTest.validationDataLocation + "omni_1212.subset.b37.vcf", testOut
+    )
+
+    spec.fileMD5s += testOut ->"28589eeb28fac753577c027abf939345"
+
+  }
+
+  @Test
+  def testVCFSimpleMerge {
+    var testOut = "vcf.simplemerge.vcf"
+    val spec = new PipelineTestSpec
+    val int1 = BaseTest.validationDataLocation + "omni.subset.interleaved.1.vcf"
+    val int2 = BaseTest.validationDataLocation + "omni.subset.interleaved.2.vcf"
+    spec.name = "vcfSimpleMerge"
+    spec.args = "-S scala/qscript/oneoffs/QTools.q -T VCFSimpleMerge -vcfs %s,%s -out %s -ref %s".format(
+      int1,int2,testOut,BaseTest.b37KGReference
+    )
+
+    spec.fileMD5s += testOut -> "c59b8de64ba787a2ca3a1734bdebf277"
+  }
+
+  @Test
+  def testSortByRef {
+    var testOut = "vcf.refsorted.vcf"
+    val spec = new PipelineTestSpec
+    val unsorted = BaseTest.validationDataLocation + "omni.pos_sorted.vcf"
+    spec.name = "sortByRef"
+    spec.args = "-S scala/qscript/oneoffs/QTools.q -T SortByRef -ivcf %s -out %s -ref %s".format(
+      unsorted, testOut, BaseTest.b37KGReference
+    )
+
+    spec.fileMD5s += testOut -> "ee09af803bc94987d55d044c2ebbc0b8"
+  }
+}