Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Report on but do not error when patient has no RNA data #245

Open
wants to merge 15 commits into
base: master
Choose a base branch
from
Open

Report on but do not error when patient has no RNA data #245

wants to merge 15 commits into from

Commits on Aug 17, 2017

  1. add error classes for bamfiles not found (so they can be caught)

    @jburos
    jburos committed Aug 17, 2017
    Configuration menu
    Copy the full SHA
    08edb48 View commit details
    Browse the repository at this point in the history

  2. catch RNABamFileNotFound exceptions when processing expressed variants

    @jburos
    jburos committed Aug 17, 2017
    Configuration menu
    Copy the full SHA
    290e4a2 View commit details
    Browse the repository at this point in the history

Commits on Aug 18, 2017

  1. modify print->logger.info statements; also catch & report on no-effec… 

    …t scenario
    @jburos
    jburos committed Aug 18, 2017
    Configuration menu
    Copy the full SHA
    5985204 View commit details
    Browse the repository at this point in the history

  2. catch error in filter_effects, etc to distinguish None from 0

    @jburos
    jburos committed Aug 18, 2017
    Configuration menu
    Copy the full SHA
    7cab29f View commit details
    Browse the repository at this point in the history

  3. remove unused imports

    @jburos
    jburos committed Aug 18, 2017
    Configuration menu
    Copy the full SHA
    164c106 View commit details
    Browse the repository at this point in the history

  4. Revert "remove unused imports" 

    This reverts commit 164c106.
    @jburos
    jburos committed Aug 18, 2017
    Configuration menu
    Copy the full SHA
    7114c6e View commit details
    Browse the repository at this point in the history

  5. fix quote chars

    @jburos
    jburos committed Aug 18, 2017
    Configuration menu
    Copy the full SHA
    cd9e2ff View commit details
    Browse the repository at this point in the history

Commits on Aug 22, 2017

  1. catch missing bamfile error for expressed neoantigens

    @jburos
    jburos committed Aug 22, 2017
    Configuration menu
    Copy the full SHA
    1eb7199 View commit details
    Browse the repository at this point in the history

  2. rename error classes; add cohort config options fail_on_missing_bams,… 

    … hla, and variants
    @jburos
    jburos committed Aug 22, 2017
    Configuration menu
    Copy the full SHA
    5068cf4 View commit details
    Browse the repository at this point in the history

  3. catch errors in expressed_variant_set as well

    @jburos
    jburos committed Aug 22, 2017
    Configuration menu
    Copy the full SHA
    c0d83dc View commit details
    Browse the repository at this point in the history

  4. implement fail_on_missing_bams in filter_variants

    @jburos
    jburos committed Aug 22, 2017
    Configuration menu
    Copy the full SHA
    a670f57 View commit details
    Browse the repository at this point in the history

  5. fix lingering BamFileNotFound errors

    @jburos
    jburos committed Aug 22, 2017
    Configuration menu
    Copy the full SHA
    de9301d View commit details
    Browse the repository at this point in the history

Commits on Aug 23, 2017

  1. change repr to str?

    @jburos
    jburos committed Aug 23, 2017
    Configuration menu
    Copy the full SHA
    b7c8139 View commit details
    Browse the repository at this point in the history

Commits on Aug 30, 2017

  1. Merge branch 'master' into fix-expression-errors

    @jburos
    jburos committed Aug 30, 2017
    Configuration menu
    Copy the full SHA
    3c5e86a View commit details
    Browse the repository at this point in the history

Commits on Sep 6, 2017

  1. Merge branch 'master' into fix-expression-errors

    @jburos
    jburos committed Sep 6, 2017
    Configuration menu
    Copy the full SHA
    4a26b14 View commit details
    Browse the repository at this point in the history