[ADAM-1192] Correctly handle other whitespace in FASTA description. #1198
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heuermh
reviewed
Oct 6, 2016
| @@ -30,8 +30,8 @@ class Fasta2ADAMSuite extends ADAMFunSuite { | |||
| val contigFragments = sc.loadParquetContigFragments(convertPath) | |||
| assert(contigFragments.rdd.count() === 26) | |||
| val first = contigFragments.rdd.first() | |||
| assert(first.getContig.getContigName === "gi|224384749|gb|CM000682.1|") | |||
| assert(first.getDescription === "Homo sapiens chromosome 20, GRCh37 primary reference assembly") | |||
| assert(first.getContig.getContigName === null) | |||
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Not sure I understand, the string before the first space is typically the sequence name in FASTA format. You might want to compare to the various open-bio projects.
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Well, gi is the Entrez ID, and gb is the GenBank ID. I assure you that they are not the sequence name.
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Test FAILed. Build result: FAILUREGitHub pull request #1198 of commit 0c98c3c 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/1198/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 73f1a1cb0d8e8dee23d6ebf6b35bcb9b8881060b # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1198/merge^{commit} # timeout=10Checking out Revision 73f1a1cb0d8e8dee23d6ebf6b35bcb9b8881060b (origin/pr/1198/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 73f1a1cb0d8e8dee23d6ebf6b35bcb9b8881060bFirst 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. |
Resolves bigdatagenomics#1192. More broadly handles whitespace in the FASTA description, and also disregards FASTA metadata which is inlined.
fnothaft
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Whoops! Forgot to commit the test resource. Just pushed. |
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Test PASSed. |
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With this, recomputing the MD tags worked on the cluster with GRCh38. |
heuermh
approved these changes
Oct 7, 2016
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Thank you, @fnothaft! |
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Resolves #1192. More broadly handles whitespace in the FASTA description, and also disregards FASTA metadata which is inlined.
Testing this on the cluster as we speak.