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Merge in changes from develop. #5

Merged
merged 36 commits into from
Oct 26, 2015
Merged

Merge in changes from develop. #5

merged 36 commits into from
Oct 26, 2015

Commits on Oct 2, 2015

  1. Add coveralls to Travis YML

    Avinash Ramu committed Oct 2, 2015
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  2. Try without pyenv

    Avinash Ramu committed Oct 2, 2015
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  3. Add coveralls badge

    Avinash Ramu committed Oct 2, 2015
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  4. Add coverage flag to cmake

    Avinash Ramu committed Oct 2, 2015
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Commits on Oct 5, 2015

  1. Factor out common into function

    Avinash Ramu committed Oct 5, 2015
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Commits on Oct 6, 2015

  1. Annotate NDA, D, A with transcripts/genes

    Avinash Ramu committed Oct 6, 2015
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Commits on Oct 7, 2015

  1. Throw exceptions instead of return 1

    Avinash Ramu committed Oct 7, 2015
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Commits on Oct 8, 2015

  1. Get rid of debug statements.

    Avinash Ramu committed Oct 8, 2015
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  2. Switch to exceptions.

    Avinash Ramu committed Oct 8, 2015
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  3. Get rid of unused variable

    Avinash Ramu committed Oct 8, 2015
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Commits on Oct 12, 2015

  1. Add variants annotate command

    Avinash Ramu committed Oct 12, 2015
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  2. Make position unsigned

    Avinash Ramu committed Oct 12, 2015
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Commits on Oct 13, 2015

  1. Add annotation field

    Avinash Ramu committed Oct 13, 2015
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  2. Add constructors

    Avinash Ramu committed Oct 13, 2015
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  3. Add newline after params

    Avinash Ramu committed Oct 13, 2015
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  4. Rename location to annotation

    Avinash Ramu committed Oct 13, 2015
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  5. Rewrite overlap function with struct

    Avinash Ramu committed Oct 13, 2015
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  6. Fix include guard

    Avinash Ramu committed Oct 13, 2015
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  7. Update overlap method declaration

    Avinash Ramu committed Oct 13, 2015
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  8. Update include paths

    Avinash Ramu committed Oct 13, 2015
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  9. Add test for variants-annotate

    Avinash Ramu committed Oct 13, 2015
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Commits on Oct 15, 2015

  1. Move declaration outside loop.

    Avinash Ramu committed Oct 15, 2015
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  2. Update distance calculations.

    Avinash Ramu committed Oct 15, 2015
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  3. Remove debug annotation.

    Avinash Ramu committed Oct 15, 2015
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  4. Update expected output.

    Avinash Ramu committed Oct 15, 2015
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  5. Throw exception instead of assert.

    Avinash Ramu committed Oct 15, 2015
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Commits on Oct 16, 2015

  1. Update distance calculations.

    Avinash Ramu committed Oct 16, 2015
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  2. Update tests

    Avinash Ramu committed Oct 16, 2015
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  3. Handle transcripts on - strand correctly

    Avinash Ramu committed Oct 16, 2015
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  4. Test for variants on a -ve strand transcript 

    Add a couple of transcripts to a separate GTF file and use this
for the variants-annotate test.
    Avinash Ramu committed Oct 16, 2015
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Commits on Oct 22, 2015

  1. Add option to skip single exon transcripts.

    Avinash Ramu committed Oct 22, 2015
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  2. Add stderr to test message

    Avinash Ramu committed Oct 22, 2015
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  3. Reorder program options. 

    This doesn't work otherwise on OSX.
    @gatoravi
    gatoravi committed Oct 22, 2015
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Commits on Oct 26, 2015

  1. Try to get coveralls working

    @gatoravi
    gatoravi committed Oct 26, 2015
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  2. Try to fix brew issue on Linux workers.

    @gatoravi
    gatoravi committed Oct 26, 2015
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  3. use \$TRAVIS_OS_NAME

    @gatoravi
    gatoravi committed Oct 26, 2015
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