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Add indel effects #243

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Add indel effects #243

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Commits on Jul 18, 2017

  1. allow strata parameter to plot two survival curves

    @jburos
    jburos committed Jul 18, 2017
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  2. handle case of 1 group when plotting

    @jburos
    jburos committed Jul 18, 2017
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  3. label results as well as graphs

    @jburos
    jburos committed Jul 18, 2017
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  4. spacing

    @jburos
    jburos committed Jul 18, 2017
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Commits on Jul 19, 2017

  1. move strata function within plot_kmf

    @jburos
    jburos committed Jul 19, 2017
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  2. remove unused packages

    @jburos
    jburos committed Jul 19, 2017
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Commits on Jul 22, 2017

  1. refactor kmf code

    @jburos
    jburos committed Jul 22, 2017
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  2. adding parameter for join_on_left, so that both left & right fields c… 

    …an be defined for df loaders
    @jburos
    jburos committed Jul 22, 2017
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Commits on Jul 24, 2017

  1. remove leftover stuff from plot-surv-by-strata branch

    @jburos
    jburos committed Jul 24, 2017
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  2. add deprecation warning

    @jburos
    jburos committed Jul 24, 2017
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Commits on Jul 25, 2017

  1. remove error when both join_on & join_on_right given

    Jacqueline Buros committed Jul 25, 2017
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  2. Merge branch 'join-on-left' into develop

    Jacqueline Buros committed Jul 25, 2017
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  3. Merge branch 'plot-surv-by-strata' into develop

    Jacqueline Buros committed Jul 25, 2017
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Commits on Jul 27, 2017

  1. add get-blob method to gcio

    Jacqueline Buros committed Jul 27, 2017
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  2. Merge branch 'add-get-blob' into develop-rcc

    Jacqueline Buros committed Jul 27, 2017
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Commits on Aug 2, 2017

  1. add functions for frameshift-indels of various types

    @jburos
    jburos committed Aug 2, 2017
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  2. add exonic_frameshift_snv_count

    @jburos
    jburos committed Aug 2, 2017
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  3. add exonic_frameshift_variant_count

    @jburos
    jburos committed Aug 2, 2017
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Commits on Aug 15, 2017

  1. Merge branch 'master' into add-indel-effects

    @jburos
    jburos committed Aug 15, 2017
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  2. clean up minor edits; remove blob-related changes

    @jburos
    jburos committed Aug 15, 2017
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Commits on Aug 18, 2017

  1. add expressed exonic indel-related functions

    @jburos
    jburos committed Aug 18, 2017
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Commits on Aug 23, 2017

  1. remove extraneous frameshift functions

    @jburos
    jburos committed Aug 23, 2017
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  2. refactor function code

    @jburos
    jburos committed Aug 23, 2017
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  3. functions now always return effects, so that all filters can be chained

    @jburos
    jburos committed Aug 23, 2017
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Commits on Aug 24, 2017

  1. make separate cohorts.cohort.caching logger; move _hash_filter_fn & r… 

    …elated code to utils; error if variant_file exists but cannot be loaded
    @jburos
    jburos committed Aug 24, 2017
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  2. make sure kwargs get passed through to filter_fn; give bunch of lambd… 

    …a-functions names
    @jburos
    jburos committed Aug 24, 2017
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  3. add logger

    @jburos
    jburos committed Aug 24, 2017
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  4. memoize hash function, to save on repeated calls

    @jburos
    jburos committed Aug 24, 2017
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Commits on Aug 25, 2017

  1. fix frameshift

    @jburos
    jburos committed Aug 25, 2017
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Commits on Aug 30, 2017

  1. Merge branch 'master' into add-indel-effects

    @jburos
    jburos committed Aug 30, 2017
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