[ADAM-1083] Cleaning up org.bdgenomics.adam.models.
#1267
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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/1267/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 7ffa285253ccc23de7b9d9d7bf1a630c1502ddab # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1267/merge^{commit} # timeout=10Checking out Revision 7ffa285253ccc23de7b9d9d7bf1a630c1502ddab (origin/pr/1267/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 7ffa285253ccc23de7b9d9d7bf1a630c1502ddabFirst 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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heuermh
requested changes
Nov 15, 2016
| * | ||
| * @param regionable The input value | ||
| * @tparam U | ||
| * @return a boolean -- the input value should only participate in the regionJoin if the return value |
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@return True if ... might read better
| * corresponding information in the type of 'value', because otherwise it'd be | ||
| * difficult to extract the correct type for Byte and NumericSequence values. | ||
| * | ||
| * This class is roughly analogous to Picard's SAMTagAndValue. |
| */ | ||
| def reverseComplement(s: String, notFound: (Char => Symbol) = ((c: Char) => Symbol(c, c))) = { | ||
| s.map(x => Try(apply(x)).getOrElse(notFound(x)).complement).reverse | ||
| } | ||
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| /** number of symbols in the alphabet */ | ||
| /** | ||
| * The number of symbols in the alphabet |
| def contains(other: ReferenceRegion): Boolean = { | ||
| orientation == other.orientation && | ||
| referenceName == other.referenceName && | ||
| start <= other.start && end >= other.end | ||
| } | ||
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| /** | ||
| * Checks is our region overlaps (wholly or partially) another region. |
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Test PASSed. |
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Test PASSed. |
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Along with bigdatagenomics#1263 and bigdatagenomics#1264, this resolves bigdatagenomics#1083. * Removing unused org.bdgenomics.adam.models.ReadBucket class. * Move org.bdgenomics.adam.models.ReferencePositionPair and org.bdgenomics.adam.models.SingleReadBucket in to org.bdgenomics.adam.rdd.read and make package private. * Clean up duplicated methods and methods that were incorrectly in companion singleton for SequenceDictionary and ReadGroupDictionary. * Removed all SamReader references. * Make writable file headers private to ADAM. * Eliminated manual VCF parsing code in SnpTable. * Cleaned up scaladoc for all classes and singleton objects. * Moved `NonoverlappingRegions` test code out of `InnerBroadcastRegionJoinSuite`.
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Thanks for the review @heuermh! I've addressed your comments, rebased, and pushed. |
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Test PASSed. |
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Thank you, @fnothaft! |
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Along with #1263 and #1264, this resolves #1083.
NonoverlappingRegionstest code out ofInnerBroadcastRegionJoinSuite.