[ADAM-1083] Cleaning up `org.bdgenomics.adam.models`. #1267

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fnothaft commented Nov 15, 2016

Along with #1263 and #1264, this resolves #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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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'
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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.

@heuermh

Minor nits. Thank you for the heroic documentation efforts, my friend. :)

+ *
+ * @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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heuermh Nov 15, 2016

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@return True if ... might read better

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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.

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heuermh Nov 15, 2016

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Picard → htsjdk

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Picard → htsjdk

*/
def reverseComplement(s: String, notFound: (Char => Symbol) = ((c: Char) => Symbol(c, c))) = {
s.map(x => Try(apply(x)).getOrElse(notFound(x)).complement).reverse
}
- /** number of symbols in the alphabet */
+ /**
+ * The number of symbols in the alphabet

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end with period

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end with period

def contains(other: ReferenceRegion): Boolean = {
orientation == other.orientation &&
referenceName == other.referenceName &&
start <= other.start && end >= other.end
}
+ /**
+ * Checks is our region overlaps (wholly or partially) another region.

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is → if

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is → if

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[ADAM-1083] Cleaning up `org.bdgenomics.adam.models`.
Along with #1263 and #1264, this resolves #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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fnothaft commented Nov 16, 2016

Thanks for the review @heuermh! I've addressed your comments, rebased, and pushed.

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@heuermh heuermh merged commit c1b4b7d into bigdatagenomics:master Nov 16, 2016

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Thank you, @fnothaft!

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heuermh commented Nov 16, 2016

Thank you, @fnothaft!

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