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Reconfigure how SNV-callers uses BED files for TMB calculations #671

Merged
merged 20 commits into from
Apr 15, 2020
Merged

Reconfigure how SNV-callers uses BED files for TMB calculations #671

merged 20 commits into from
Apr 15, 2020

Commits on Apr 3, 2020

  1. Copies of old stuff that I can take pieces from

    @cansavvy
    cansavvy committed Apr 3, 2020
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  2. BED ranges set up

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    cansavvy committed Apr 3, 2020
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  3. It's mostly working!

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    cansavvy committed Apr 3, 2020
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  4. Few tinier edits before testing

    @cansavvy
    cansavvy committed Apr 3, 2020
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  5. Change back to normal files

    @cansavvy
    cansavvy committed Apr 3, 2020
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  6. Get rid of old scripts.

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    cansavvy committed Apr 3, 2020
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  7. Development remnant

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    cansavvy committed Apr 3, 2020
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  8. Run styler on it all!

    @cansavvy
    cansavvy committed Apr 3, 2020
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  9. Change back the indexing change that apparently HGG was dependent on

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    cansavvy committed Apr 3, 2020
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Commits on Apr 6, 2020

  1. Retire old analyses from CircleCI

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    cansavvy committed Apr 6, 2020
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  2. Merge remote-tracking branch 'cbethell/master' into tcga-bed-files

    @cansavvy
    cansavvy committed Apr 6, 2020
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  3. Add back TCGA processing

    @cansavvy
    cansavvy committed Apr 6, 2020
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Commits on Apr 8, 2020

  1. Incorporate @jashapiro doc and tidy suggestions

    @cansavvy
    cansavvy committed Apr 8, 2020
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  2. Add TODOs to things we won't do just yet.

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    cansavvy committed Apr 8, 2020
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Commits on Apr 9, 2020

  1. genome_size -> region_size

    @cansavvy
    cansavvy committed Apr 9, 2020
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  2. Write down 256GB to figures README

    @cansavvy
    cansavvy committed Apr 9, 2020
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  3. Drop Panel samples in calculate TMB

    @cansavvy
    cansavvy committed Apr 9, 2020
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  4. Use a better fix for the Panel problem

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    cansavvy committed Apr 9, 2020
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Commits on Apr 13, 2020

  1. Merge branch 'master' into tcga-bed-files

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    cansavvy authored Apr 13, 2020
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  2. Refresh plot

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    cansavvy committed Apr 13, 2020
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