72 lines
2.4 KiB
Scala
Executable File
72 lines
2.4 KiB
Scala
Executable File
package org.broadinstitute.sting.queue.pipeline
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import org.testng.annotations.Test
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import org.broadinstitute.sting.BaseTest
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class IPFLibraryPipelineTest {
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@Test
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def testVCFExtractSites {
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var testOut = "vcfes.vcf"
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val spec = new PipelineTestSpec
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spec.name = "vcfExtractSites"
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spec.args = "-S scala/qscript/oneoffs/QTools.q -T VCFExtractSites -ivcf %s -out %s".format(
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BaseTest.validationDataLocation + "omni_1212.subset.b37.vcf", testOut
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)
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spec.fileMD5s += testOut -> "4f496b8cf90302428a9edda486a337f4"
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PipelineTest.executeTest(spec)
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}
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@Test
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def testVCFExtractSamples {
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var testOut = "vcf.extract.samples.vcf"
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val spec = new PipelineTestSpec
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spec.name = "vcfExtractSamples"
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spec.args = "-S scala/qscript/oneoffs/QTools.q -T VCFExtractSamples -ivcf %s -out %s -sm HG00107,HG00500,NA18501,NA18942".format(
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BaseTest.validationDataLocation + "omni_1212.subset.b37.vcf", testOut
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)
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spec.fileMD5s += testOut -> "180d5a2e7a1fbc5117de6705bde3a7c8"
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}
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@Test
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def testVCFExtractIntervals {
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var testOut = "vcf.extract.intervals.list"
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val spec = new PipelineTestSpec
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spec.name = "vcfExtractIntervals"
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spec.args = "-S scala/qscript/oneoffs/QTools.q -T VCFExtractIntervals -ivcf %s -out %s".format(
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BaseTest.validationDataLocation + "omni_1212.subset.b37.vcf", testOut
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)
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spec.fileMD5s += testOut ->"28589eeb28fac753577c027abf939345"
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}
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@Test
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def testVCFSimpleMerge {
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var testOut = "vcf.simplemerge.vcf"
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val spec = new PipelineTestSpec
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val int1 = BaseTest.validationDataLocation + "omni.subset.interleaved.1.vcf"
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val int2 = BaseTest.validationDataLocation + "omni.subset.interleaved.2.vcf"
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spec.name = "vcfSimpleMerge"
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spec.args = "-S scala/qscript/oneoffs/QTools.q -T VCFSimpleMerge -vcfs %s,%s -out %s -ref %s".format(
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int1,int2,testOut,BaseTest.b37KGReference
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)
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spec.fileMD5s += testOut -> "c59b8de64ba787a2ca3a1734bdebf277"
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}
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@Test
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def testSortByRef {
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var testOut = "vcf.refsorted.vcf"
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val spec = new PipelineTestSpec
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val unsorted = BaseTest.validationDataLocation + "omni.pos_sorted.vcf"
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spec.name = "sortByRef"
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spec.args = "-S scala/qscript/oneoffs/QTools.q -T SortByRef -ivcf %s -out %s -ref %s".format(
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unsorted, testOut, BaseTest.b37KGReference
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)
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spec.fileMD5s += testOut -> "ee09af803bc94987d55d044c2ebbc0b8"
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}
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}
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