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Merged bug fix from Stable into Unstable

This commit is contained in:
David Roazen 2011-07-01 13:53:46 -04:00
parent 7159b14e76 11d4af0e75
commit 350a76d5dd
3 changed files with 4 additions and 75 deletions
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71
public/scala/test/org/broadinstitute/sting/queue/pipeline/IPFLibraryPipelineTest.scala
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@ -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"
}
}

2
public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociPipelineTest.scala
View File

@ -35,7 +35,7 @@ class ExampleCountLociPipelineTest {
val spec = new PipelineTestSpec
spec.name = "countloci"
spec.args = Array(
" -S scala/qscript/examples/ExampleCountLoci.scala",
" -S public/scala/qscript/examples/ExampleCountLoci.scala",
" -R " + BaseTest.hg18Reference,
" -I " + BaseTest.validationDataLocation + "small_bam_for_countloci.bam",
" -o " + testOut).mkString

6
public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldPipelineTest.scala
View File

@ -32,7 +32,7 @@ class HelloWorldPipelineTest {
def testHelloWorld {
val spec = new PipelineTestSpec
spec.name = "HelloWorld"
spec.args = "-S scala/qscript/examples/HelloWorld.scala"
spec.args = "-S public/scala/qscript/examples/HelloWorld.scala"
PipelineTest.executeTest(spec)
}
@ -40,7 +40,7 @@ class HelloWorldPipelineTest {
def testHelloWorldWithPrefix {
val spec = new PipelineTestSpec
spec.name = "HelloWorldWithPrefix"
spec.args = "-S scala/qscript/examples/HelloWorld.scala -jobPrefix HelloWorld"
spec.args = "-S public/scala/qscript/examples/HelloWorld.scala -jobPrefix HelloWorld"
PipelineTest.executeTest(spec)
}
@ -48,7 +48,7 @@ class HelloWorldPipelineTest {
def testHelloWorldWithPriority {
val spec = new PipelineTestSpec
spec.name = "HelloWorldWithPriority"
spec.args = "-S scala/qscript/examples/HelloWorld.scala -jobPriority 100"
spec.args = "-S public/scala/qscript/examples/HelloWorld.scala -jobPriority 100"
PipelineTest.executeTest(spec)
}
}