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Major fix and feature expansion #24

Merged
merged 26 commits into from
Oct 13, 2018
Merged

Major fix and feature expansion #24

merged 26 commits into from
Oct 13, 2018

Commits on Sep 18, 2018

  1. working on csi format support

    @betteridiot
    betteridiot committed Sep 18, 2018
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Commits on Sep 19, 2018

  1. Merge branch 'master' into csi_dev

    @betteridiot
    betteridiot committed Sep 19, 2018
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  2. updating csi_dev utils

    @betteridiot
    betteridiot committed Sep 19, 2018
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  3. updating CSI support

    @betteridiot
    betteridiot committed Sep 19, 2018
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  4. adding extension info

    @betteridiot
    betteridiot committed Sep 19, 2018
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  5. correcting hard coded path

    @betteridiot
    betteridiot committed Sep 19, 2018
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  6. messing with Travis CI

    @betteridiot
    betteridiot committed Sep 19, 2018
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  7. more messing

    @betteridiot
    betteridiot committed Sep 19, 2018
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  8. still messing with tci

    @betteridiot
    betteridiot committed Sep 19, 2018
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  9. travis ci is being a pain

    @betteridiot
    betteridiot committed Sep 19, 2018
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  10. tci

    @betteridiot
    betteridiot committed Sep 19, 2018
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  11. tci

    @betteridiot
    betteridiot committed Sep 19, 2018
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  12. ugh

    @betteridiot
    betteridiot committed Sep 19, 2018
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  13. Trying some more tci

    @betteridiot
    betteridiot committed Sep 19, 2018
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  14. whoops

    @betteridiot
    betteridiot committed Sep 19, 2018
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  15. Giving up on TCI py37 for now

    @betteridiot
    betteridiot committed Sep 19, 2018
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  16. Added additional boundary conditions on .fetch() 

    Fetch was not filtering out reads that were *before* the region, just the ones after.
    @betteridiot
    betteridiot committed Sep 19, 2018
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Commits on Sep 20, 2018

  1. Updating pytests

    @betteridiot
    betteridiot committed Sep 20, 2018
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  2. Updating csi_dev from master

    @betteridiot
    betteridiot committed Sep 20, 2018
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  3. Pytest acting funny

    @betteridiot
    betteridiot committed Sep 20, 2018
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  4. BAM output 

    This should be the first steps towards fully supporting BAM output mentioned in #5
    @betteridiot
    betteridiot committed Sep 20, 2018
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  5. replaced bytearray.insert for [0:0]

    @betteridiot
    betteridiot committed Sep 20, 2018
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  6. updating read for loop bug

    @betteridiot
    betteridiot committed Sep 20, 2018
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Commits on Sep 21, 2018

  1. Added .to_bam() to core.AlignedSegment

    @betteridiot
    betteridiot committed Sep 21, 2018
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Commits on Oct 12, 2018

  1. Major restructuring of random access 

    There was a deleterious flaw in the random access algorithm that was causing the file cursor to start way to the right of regions if interest.
    @betteridiot
    betteridiot committed Oct 12, 2018
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Commits on Oct 13, 2018

  1. fixing pytest

    @betteridiot
    betteridiot committed Oct 13, 2018
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