From 11d4af0e7528d0d3dd8b5da3745ad7d7bced7280 Mon Sep 17 00:00:00 2001
From: David Roazen <droazen@broadinstitute.org>
Date: Fri, 1 Jul 2011 13:41:34 -0400
Subject: [PATCH] Path-related fixes to the private queue pipeline tests.

---
 .../pipeline/IPFLibraryPipelineTest.scala     | 71 -------------------
 1 file changed, 71 deletions(-)
 delete mode 100755 public/scala/test/org/broadinstitute/sting/queue/pipeline/IPFLibraryPipelineTest.scala

diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/IPFLibraryPipelineTest.scala b/public/scala/test/org/broadinstitute/sting/queue/pipeline/IPFLibraryPipelineTest.scala
deleted file mode 100755
index 6b32e5c9d..000000000
--- a/public/scala/test/org/broadinstitute/sting/queue/pipeline/IPFLibraryPipelineTest.scala
+++ /dev/null
@@ -1,71 +0,0 @@
-package org.broadinstitute.sting.queue.pipeline
-
-import org.testng.annotations.Test
-import org.broadinstitute.sting.BaseTest
-
-class IPFLibraryPipelineTest {
-
-  @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"
-  }
-}