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Sub commands #9

Merged
merged 18 commits into from
Mar 7, 2018
Merged

Sub commands #9

merged 18 commits into from
Mar 7, 2018

Commits on Mar 3, 2018

  1. start of refactoring

    @brentp
    brentp committed Mar 3, 2018
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  2. more progress on refactor

    @brentp
    brentp committed Mar 3, 2018
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  3. lumpy as standalone

    @brentp
    brentp committed Mar 3, 2018
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  4. incremental fixes

    @brentp
    brentp committed Mar 3, 2018
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Commits on Mar 5, 2018

  1. single CLI

    @brentp
    brentp committed Mar 5, 2018
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  2. still run other filters even without mosdepth

    @brentp
    brentp committed Mar 5, 2018
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  3. allow lumpy to use svtyper directly

    @brentp
    brentp committed Mar 5, 2018
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  4. filter BNDs with too little support

    @brentp
    brentp committed Mar 5, 2018
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  5. add BND filtering inside of lumpy

    @brentp
    brentp committed Mar 5, 2018
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  6. allow skipping extra filters

    @brentp
    brentp committed Mar 5, 2018
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  7. add merge command and allow svtyper to keep reference calls

    @brentp
    brentp committed Mar 5, 2018
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Commits on Mar 6, 2018

  1. rename everything to smoove

    @brentp
    brentp committed Mar 6, 2018
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  2. show installed software in main command

    @brentp
    brentp committed Mar 6, 2018
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  3. filter cnvnator calls on q0 column

    @brentp
    brentp committed Mar 6, 2018
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Commits on Mar 7, 2018

  1. check file sizes in paste 

    also small opt in svtyper
    @brentp
    brentp committed Mar 7, 2018
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  2. parallelization fixes

    @brentp
    brentp committed Mar 7, 2018
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  3. more error checking

    @brentp
    brentp committed Mar 7, 2018
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  4. update readme with new setup

    @brentp
    brentp committed Mar 7, 2018
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