add function:filterByOverlappingRegions #1287
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for multiple regions data select.
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Can one of the admins verify this patch? |
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Jenkins, test this please |
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Test FAILed. Build result: FAILURE[...truncated 3 lines...]Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git -c core.askpass=true fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git -c core.askpass=true fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1287/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 57397933361bd4535c372f6c54dfa496a16372a2 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1287/merge^{commit} # timeout=10Checking out Revision 57397933361bd4535c372f6c54dfa496a16372a2 (origin/pr/1287/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 57397933361bd4535c372f6c54dfa496a16372a2First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Test FAILed. |
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From the failed Jenkins build |
fnothaft
requested changes
Nov 21, 2016
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| querys.map(query => { | ||
| regions.exists(_.overlaps(query)) | ||
| }).reduce((a, b) => a || b) |
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I would replace reduce((a, b) => a || b) with fold(false)((a, b) => a || b) as reduce will fail on an empty collection. You can get an empty result from getReferenceRegions(elem) with unmapped reads.
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This is a very helpful advise, Thanks!
| @@ -106,6 +106,16 @@ class AlignmentRecordRDDSuite extends ADAMFunSuite { | |||
| assert(coverage.rdd.filter(r => r.start == 30).first.count == pointCoverage) | |||
| } | |||
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| sparkTest("test filterByOverlappingRegions") { | |||
| val inputPath = resourcePath("artificial.sam") | |||
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You'll want to change resourcePath("artificial.sam") to testFile("artificial.sam") and then this should compile.
fnothaft
approved these changes
Nov 22, 2016
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Jenkins, test this please. |
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Test PASSed. |
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Merged! Thank you very much @liamlee for the contribution! |
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My pleasure. |
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for multiple regions data select.