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Adding in codec to read from Gencode GTF files. Fixes #3277 #3410

Merged
merged 8 commits into from
Sep 18, 2017
Merged

Adding in codec to read from Gencode GTF files. Fixes #3277 #3410

merged 8 commits into from
Sep 18, 2017

Commits on Sep 12, 2017

  1. Adding in codec to read from Gencode GTF files. Fixes #3277 

    Includes tests for both hg19 and hg38.
    @jonn-smith
    jonn-smith committed Sep 12, 2017
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  2. Fixing a warning in the test suite.

    @jonn-smith
    jonn-smith committed Sep 12, 2017
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  3. Addressing the first of the code review comments.

    @jonn-smith
    jonn-smith committed Sep 12, 2017
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  4. Addressing latest code review comments. 

    Also cleaned up some warnings (e.g. non-final fields became final).
    @jonn-smith
    jonn-smith committed Sep 12, 2017
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  5. Added in a UCSC version number to GencodeGtfFeature.

    @jonn-smith
    jonn-smith committed Sep 12, 2017
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  6. Refactored GencodeGtfFeature::contains to take <T extends Locatable>.

    @jonn-smith
    jonn-smith committed Sep 12, 2017
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Commits on Sep 13, 2017

  1. Added GencodeGtfFeature::overlaps (leverages SimpleInterval::overlaps).

    @jonn-smith
    jonn-smith committed Sep 13, 2017
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  2. Fixing unnecessary generic.

    @jonn-smith
    jonn-smith committed Sep 13, 2017
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