Refactored SequenceDictionary #162
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All automated tests passed. |
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Jenkins, test this please. |
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Matt, I think this needs to be rebased before we test it. I can't get to that today, but will do it tomorrow. |
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All automated tests passed. |
…tween RDD extensions, and to improve speed. Additionally, refactored SequenceDictionary class to reduce GC overhead and to make class immutable.
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This is rebased and ready for merge. Jenkins, test this please. |
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All automated tests passed. |
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Thanks, Frank! |
massie
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Apr 3, 2014
This commit fixes issue bigdatagenomics#162. Adam --> ADAM for all file contents and file names. All scala code reformatted with https://github.com/mdr/scalariform/wiki/Command-line-tool
massie
pushed a commit
that referenced
this pull request
Apr 3, 2014
The commits fix issue #162. Adam --> ADAM for all file contents and file names. All scala code reformatted with https://github.com/mdr/scalariform/wiki/Command-line-tool
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Refactored aggregation to eliminate replication between RDD extensions, and to improve speed. Additionally, refactored SequenceDictionary class to reduce GC overhead and to make class immutable. GC overhead was reduced by switching away from pointer based data structures to arrays. Additionally, eliminated "derived" sequences from inside of SequenceDictionary.