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Generate signatures from 10x single cell bam file #539

Merged
merged 24 commits into from
Oct 1, 2018
Merged

Generate signatures from 10x single cell bam file #539

merged 24 commits into from
Oct 1, 2018

Commits on Sep 1, 2018

  1. Add bam files for testing

    @olgabot
    olgabot committed Sep 1, 2018
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  2. Add reading 10x bam files

    @olgabot
    olgabot committed Sep 1, 2018
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  3. Add pysam to requirements

    @olgabot
    olgabot committed Sep 1, 2018
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  4. Add sourmash compute test

    @olgabot
    olgabot committed Sep 1, 2018
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Commits on Sep 2, 2018

  1. Move test data to actually be like the 10x structure

    @olgabot
    olgabot committed Sep 2, 2018
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  2. tests pass!

    @olgabot
    olgabot committed Sep 2, 2018
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  3. avoid direct dep on pysam, fix tests and argparse in commands

    @luizirber
    luizirber committed Sep 2, 2018
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  4. Add updated test data location

    @olgabot
    olgabot committed Sep 2, 2018
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  5. Skip 10x test if pysam isn't installed

    @olgabot
    olgabot committed Sep 2, 2018
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  6. Merge pull request #1 from luizirber/fix_tests 

    avoid direct dep on pysam
    @olgabot
    olgabot committed Sep 2, 2018
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Commits on Sep 4, 2018

  1. Add "import pytest"

    @olgabot
    olgabot committed Sep 4, 2018
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Commits on Sep 6, 2018

  1. Move testing of alignment into function

    @olgabot
    olgabot committed Sep 6, 2018
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  2. Move import to top of file

    @olgabot
    olgabot committed Sep 6, 2018
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Commits on Sep 7, 2018

  1. Try doing some multiprocessing

    @olgabot
    olgabot committed Sep 7, 2018
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Commits on Sep 14, 2018

  1. Add threads to arguments

    @olgabot
    olgabot committed Sep 14, 2018
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  2. Add pathos to requirements

    @olgabot
    olgabot committed Sep 14, 2018
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  3. Remove pysam, add bamnostic

    @olgabot
    olgabot committed Sep 14, 2018
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  4. add type for threads argument

    @olgabot
    olgabot committed Sep 14, 2018
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  5. lung_ptprc --> 10x-example

    @olgabot
    olgabot committed Sep 14, 2018
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Commits on Sep 17, 2018

  1. Specify version of bamnostic

    @olgabot
    olgabot committed Sep 17, 2018
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  2. multiprocessing.Pool isn't a context manager in Python2.7

    @olgabot
    olgabot committed Sep 17, 2018
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  3. Skip 10x test only if bamnostic not installed

    @olgabot
    olgabot committed Sep 17, 2018
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Commits on Sep 18, 2018

  1. Increase bamnostic version

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

  1. Merge branch 'master' into olgabot/10x-singlecell-bam

    @olgabot
    olgabot committed Sep 19, 2018
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