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Remove obsolete unmapped reads test for FindCoveredIntervals (#1580) 

Remove obsolete unmapped reads test for FindCoveredIntervals
This commit is contained in:
Ron Levine 2017-05-02 08:50:12 -04:00 committed by GitHub
parent 31eee1f2a3
commit 505383e504
2 changed files with 0 additions and 20 deletions
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16
protected/gatk-queue-extensions-distribution/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/UnmappedExcludedQueueTest.scala
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@ -60,22 +60,6 @@ class UnmappedExcludedQueueTest {
@Test(timeOut=36000000)
def testUnmappedExclusion(): Unit = {
//FindCoveredIntervals is an ActiveRegionWalker, which throws an exception if it encounters unmapped reads
//But it's partitioned by contigs, which by default includes unmapped reads. Verify that the unmapped reads
//are correctly not added in this case
val testOut = "fci.out"
val spec = new QueueTestSpec
spec.name = "findcoveredintervals"
spec.args = Array(
" -S " + QueueTest.protectedQScriptsPackageDir + "examples/ExampleFindCoveredIntervals.scala",
" -R " + BaseTest.publicTestDir + "exampleFASTA.fasta",
" -I " + BaseTest.publicTestDir + "exampleBAM.bam",
" -out " + testOut).mkString
//The output file is blank - the real test is simply that it runs to completion
spec.fileMD5s += testOut -> "d41d8cd98f00b204e9800998ecf8427e"
QueueTest.executeTest(spec)
//Regression Test: HaplotypeCaller is also an ActiveRegionWalker, and is much more widely used. Explicitly test
//it as well
val hcTestOut = "hctest.vcf"

4
public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ActiveRegionWalker.java
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@ -189,10 +189,6 @@ public abstract class ActiveRegionWalker<MapType, ReduceType> extends Walker<Map
return desiredReadStates().contains(ActiveRegionReadState.EXTENDED);
}
public boolean wantsUnmappedReads() {
return desiredReadStates().contains(ActiveRegionReadState.UNMAPPED);
}
// Determine probability of active status over the AlignmentContext
@Ensures({"result.isActiveProb >= 0.0", "result.isActiveProb <= 1.0"})
public abstract ActivityProfileState isActive(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context);