Extended TwoBitFile and NucleotideContigFragmentRDDFunctions to behave more similar #1079

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akmorrow13 commented Jul 13, 2016

  • Extended NucleotideContigFragmentRDDFunctions to ReferenceFile
  • Added getSequenceDictionary function to TwoBitFile
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Test FAILed.
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Build result: FAILURE

GitHub pull request #1079 of commit e035ee9 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prb > /home/jenkins/git2/bin/git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > /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 --version # timeout=10 > /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/1079/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 1084b30 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1079/merge^{commit} # timeout=10Checking out Revision 1084b30 (origin/pr/1079/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 1084b305f73d732332930a9109f54a75be4956bbFirst 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.

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1337/

Build result: FAILURE

GitHub pull request #1079 of commit e035ee9 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prb > /home/jenkins/git2/bin/git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > /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 --version # timeout=10 > /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/1079/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 1084b30 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1079/merge^{commit} # timeout=10Checking out Revision 1084b30 (origin/pr/1079/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 1084b305f73d732332930a9109f54a75be4956bbFirst 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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@akmorrow13 let's chat about this sometime. NucleotideContigFragmentRDDFunctions goes away in #1051 . The possibly misnamed ReferenceContigMap class may be sufficient for your needs.

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fnothaft commented Jul 13, 2016

@akmorrow13 let's chat about this sometime. NucleotideContigFragmentRDDFunctions goes away in #1051 . The possibly misnamed ReferenceContigMap class may be sufficient for your needs.

+ def getSequenceDictionary(performLexSort: Boolean = false): SequenceDictionary = {
+ val sd = new SequenceDictionary(seqRecords.toVector.map(r => SequenceRecord(r._1, r._2.dnaSize)))
+
+ if (performLexSort) {

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Why's this necessary?

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fnothaft Jul 13, 2016

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Why's this necessary?

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akmorrow13 Jul 13, 2016

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I need the sequence dictionary from 2 bit file. Is there a better way to get it?

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akmorrow13 Jul 13, 2016

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I need the sequence dictionary from 2 bit file. Is there a better way to get it?

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fnothaft Jul 14, 2016

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Oh, yeah, that makes sense. My comment was with regards to the lexicographic sort.

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fnothaft Jul 14, 2016

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Oh, yeah, that makes sense. My comment was with regards to the lexicographic sort.

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fnothaft Jul 14, 2016

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IIRC, we've added lex sort functions to the SequenceDictionary, so I'd rather not dupe the code.

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fnothaft Jul 14, 2016

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IIRC, we've added lex sort functions to the SequenceDictionary, so I'd rather not dupe the code.

@akmorrow13 akmorrow13 closed this Jul 18, 2016

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