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Fix improper dependencies in QScripts used by pipeline tests, and att…

…empt to fix the flawed MisencodedBaseQualityUnitTest

-Some QScripts used by public pipeline tests unnecessarily used the (now protected) UnifiedGenotyper.
 Changed them to use PrintReads instead.

-Moved ExampleUnifiedGenotyperPipelineTest to protected

-Attempt to fix the flawed and sporadically failing MisencodedBaseQualityUnitTest:

   After looking at this class a bit, I think the problem was the use of global arrays for the quals
   shared across all reads in all tests (BAMRecord class definitely does not make a separate copy for
   each read!). One test (testFixBadQuals) modifies the bad quals array, and if this happens to run
   before the testBadQualsThrowsError test the bad quals array will have been "fixed" and no exception
   will be thrown.
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1 parent 12a3d7e commit 2a7af4316478348f7ea58e0803b3391593d6dbd6 @droazen droazen committed Feb 27, 2013
@@ -0,0 +1,117 @@
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+
+package org.broadinstitute.sting.queue.pipeline.examples
+
+import org.testng.annotations.{DataProvider, Test}
+import org.broadinstitute.sting.queue.pipeline.{PipelineTest, PipelineTestSpec}
+import org.broadinstitute.sting.BaseTest
+
+class ExampleUnifiedGenotyperPipelineTest {
+ @Test(timeOut=36000000)
+ def testUnifiedGenotyper() {
+ val spec = new PipelineTestSpec
+ spec.name = "unifiedgenotyper"
+ spec.args = Array(
+ " -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala",
+ " -R " + BaseTest.publicTestDir + "exampleFASTA.fasta",
+ " -I " + BaseTest.publicTestDir + "exampleBAM.bam",
+ " -filter QD",
+ " -filterExpression 'QD < 2.0'").mkString
+ spec.jobRunners = PipelineTest.allJobRunners
+ PipelineTest.executeTest(spec)
+ }
+
+ @DataProvider(name = "ugIntervals")
+ def getUnifiedGenotyperIntervals =
+ Array(
+ Array("gatk_intervals", BaseTest.validationDataLocation + "intervalTest.intervals"),
+ Array("bed_intervals", BaseTest.validationDataLocation + "intervalTest.bed"),
+ Array("vcf_intervals", BaseTest.validationDataLocation + "intervalTest.1.vcf")
+ ).asInstanceOf[Array[Array[Object]]]
+
+ @Test(dataProvider = "ugIntervals", timeOut=36000000)
+ def testUnifiedGenotyperWithIntervals(intervalsName: String, intervalsPath: String) {
+ val spec = new PipelineTestSpec
+ spec.name = "unifiedgenotyper_with_" + intervalsName
+ spec.args = Array(
+ " -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala",
+ " -I " + BaseTest.validationDataLocation + "OV-0930.normal.chunk.bam",
+ " -R " + BaseTest.hg18Reference,
+ " -L " + intervalsPath).mkString
+ spec.jobRunners = Seq("Lsf706")
+ PipelineTest.executeTest(spec)
+ }
+
+ @Test(timeOut=36000000)
+ def testUnifiedGenotyperNoGCOpt() {
+ val spec = new PipelineTestSpec
+ spec.name = "unifiedgenotyper_no_gc_opt"
+ spec.args = Array(
+ " -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala",
+ " -R " + BaseTest.publicTestDir + "exampleFASTA.fasta",
+ " -I " + BaseTest.publicTestDir + "exampleBAM.bam",
+ " -noGCOpt").mkString
+ spec.jobRunners = PipelineTest.allJobRunners
+ PipelineTest.executeTest(spec)
+ }
+
+ @DataProvider(name="resMemReqParams")
+ def getResMemReqParam = Array(Array("mem_free"), Array("virtual_free")).asInstanceOf[Array[Array[Object]]]
+
+ @Test(dataProvider = "resMemReqParams", timeOut=36000000)
+ def testUnifiedGenotyperResMemReqParam(reqParam: String) {
+ val spec = new PipelineTestSpec
+ spec.name = "unifiedgenotyper_" + reqParam
+ spec.args = Array(
+ " -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala",
+ " -R " + BaseTest.publicTestDir + "exampleFASTA.fasta",
+ " -I " + BaseTest.publicTestDir + "exampleBAM.bam",
+ " -resMemReqParam " + reqParam).mkString
+ spec.jobRunners = Seq("GridEngine")
+ PipelineTest.executeTest(spec)
+ }
+}
@@ -34,6 +34,7 @@
import org.testng.annotations.Test;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.List;
/**
@@ -55,7 +56,9 @@ public void before() {
}
private GATKSAMRecord createRead(final boolean useGoodBases) {
- GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "foo", 0, 10, readBases.getBytes(), useGoodBases ? goodQuals : badQuals);
+ GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "foo", 0, 10, readBases.getBytes(),
+ useGoodBases ? Arrays.copyOf(goodQuals, goodQuals.length) :
+ Arrays.copyOf(badQuals, badQuals.length));
read.setCigarString("10M");
return read;
}
@@ -39,12 +39,12 @@ class DevNullOutput extends QScript {
var bamFile: File = _
def script() {
- val genotyper = new UnifiedGenotyper
- genotyper.reference_sequence = referenceFile
- genotyper.memoryLimit = 2
- genotyper.scatterCount = 3
- genotyper.input_file :+= bamFile
- genotyper.out = "/dev/null"
- add(genotyper)
+ val printReads = new PrintReads
+ printReads.reference_sequence = referenceFile
+ printReads.memoryLimit = 2
+ printReads.scatterCount = 3
+ printReads.input_file :+= bamFile
+ printReads.out = "/dev/null"
+ add(printReads)
}
}
@@ -29,7 +29,7 @@ import org.broadinstitute.sting.queue.QScript
import org.broadinstitute.sting.queue.extensions.gatk._
/**
- * Script used for testing output to /dev/null
+ * Script used for testing inclusion of a read filter
*/
class ExampleReadFilter extends QScript {
@Input(doc="The reference file for the bam files.", shortName="R")
@@ -39,10 +39,10 @@ class ExampleReadFilter extends QScript {
var bamFile: File = _
def script() {
- val genotyper = new UnifiedGenotyper with BadMate
- genotyper.reference_sequence = referenceFile
- genotyper.memoryLimit = 2
- genotyper.input_file :+= bamFile
- add(genotyper)
+ val printReads = new PrintReads with BadMate
+ printReads.reference_sequence = referenceFile
+ printReads.memoryLimit = 2
+ printReads.input_file :+= bamFile
+ add(printReads)
}
}
@@ -33,21 +33,21 @@ class ExampleRetryMemoryLimit extends QScript {
@Input(doc="The reference file for the bam files.", shortName="R")
var referenceFile: File = _
- @Input(doc="Bam file to genotype.", shortName="I")
+ @Input(doc="Bam file to print.", shortName="I")
var bamFile: File = _
def script() {
for (scatterCount <- 1 to 2) {
- val ug = new UnifiedGenotyper with RetryMemoryLimit
+ val printReads = new PrintReads with RetryMemoryLimit
// First run with 1m
- ug.memoryLimit = .001
+ printReads.memoryLimit = .001
// On retry run with 1g
- ug.retryMemoryFunction = (d => d * 1000)
- ug.reference_sequence = referenceFile
- ug.input_file = Seq(bamFile)
- ug.out = swapExt(bamFile, ".bam", ".scattered_%d.vcf".format(scatterCount))
- ug.scatterCount = scatterCount
- add(ug)
+ printReads.retryMemoryFunction = (d => d * 1000)
+ printReads.reference_sequence = referenceFile
+ printReads.input_file = Seq(bamFile)
+ printReads.out = swapExt(bamFile, ".bam", ".out.scattered_%d.bam".format(scatterCount))
+ printReads.scatterCount = scatterCount
+ add(printReads)
}
}
}
@@ -1,96 +0,0 @@
-/*
-* Copyright (c) 2012 The Broad Institute
-*
-* Permission is hereby granted, free of charge, to any person
-* obtaining a copy of this software and associated documentation
-* files (the "Software"), to deal in the Software without
-* restriction, including without limitation the rights to use,
-* copy, modify, merge, publish, distribute, sublicense, and/or sell
-* copies of the Software, and to permit persons to whom the
-* Software is furnished to do so, subject to the following
-* conditions:
-*
-* The above copyright notice and this permission notice shall be
-* included in all copies or substantial portions of the Software.
-*
-* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
-* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
-* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
-* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
-* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
-*/
-
-package org.broadinstitute.sting.queue.pipeline.examples
-
-import org.testng.annotations.{DataProvider, Test}
-import org.broadinstitute.sting.queue.pipeline.{PipelineTest, PipelineTestSpec}
-import org.broadinstitute.sting.BaseTest
-
-class ExampleUnifiedGenotyperPipelineTest {
- @Test(timeOut=36000000)
- def testUnifiedGenotyper() {
- val spec = new PipelineTestSpec
- spec.name = "unifiedgenotyper"
- spec.args = Array(
- " -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala",
- " -R " + BaseTest.publicTestDir + "exampleFASTA.fasta",
- " -I " + BaseTest.publicTestDir + "exampleBAM.bam",
- " -filter QD",
- " -filterExpression 'QD < 2.0'").mkString
- spec.jobRunners = PipelineTest.allJobRunners
- PipelineTest.executeTest(spec)
- }
-
- @DataProvider(name = "ugIntervals")
- def getUnifiedGenotyperIntervals =
- Array(
- Array("gatk_intervals", BaseTest.validationDataLocation + "intervalTest.intervals"),
- Array("bed_intervals", BaseTest.validationDataLocation + "intervalTest.bed"),
- Array("vcf_intervals", BaseTest.validationDataLocation + "intervalTest.1.vcf")
- ).asInstanceOf[Array[Array[Object]]]
-
- @Test(dataProvider = "ugIntervals", timeOut=36000000)
- def testUnifiedGenotyperWithIntervals(intervalsName: String, intervalsPath: String) {
- val spec = new PipelineTestSpec
- spec.name = "unifiedgenotyper_with_" + intervalsName
- spec.args = Array(
- " -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala",
- " -I " + BaseTest.validationDataLocation + "OV-0930.normal.chunk.bam",
- " -R " + BaseTest.hg18Reference,
- " -L " + intervalsPath).mkString
- spec.jobRunners = Seq("Lsf706")
- PipelineTest.executeTest(spec)
- }
-
- @Test(timeOut=36000000)
- def testUnifiedGenotyperNoGCOpt() {
- val spec = new PipelineTestSpec
- spec.name = "unifiedgenotyper_no_gc_opt"
- spec.args = Array(
- " -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala",
- " -R " + BaseTest.publicTestDir + "exampleFASTA.fasta",
- " -I " + BaseTest.publicTestDir + "exampleBAM.bam",
- " -noGCOpt").mkString
- spec.jobRunners = PipelineTest.allJobRunners
- PipelineTest.executeTest(spec)
- }
-
- @DataProvider(name="resMemReqParams")
- def getResMemReqParam = Array(Array("mem_free"), Array("virtual_free")).asInstanceOf[Array[Array[Object]]]
-
- @Test(dataProvider = "resMemReqParams", timeOut=36000000)
- def testUnifiedGenotyperResMemReqParam(reqParam: String) {
- val spec = new PipelineTestSpec
- spec.name = "unifiedgenotyper_" + reqParam
- spec.args = Array(
- " -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala",
- " -R " + BaseTest.publicTestDir + "exampleFASTA.fasta",
- " -I " + BaseTest.publicTestDir + "exampleBAM.bam",
- " -resMemReqParam " + reqParam).mkString
- spec.jobRunners = Seq("GridEngine")
- PipelineTest.executeTest(spec)
- }
-}

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