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.

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

More funcotator fixes #4783

Merged
merged 8 commits into from
May 24, 2018
Merged

More funcotator fixes #4783

merged 8 commits into from
May 24, 2018

Commits on May 22, 2018

  1. Some other fixes:

    - Ordering specified in the header did not match the variants and hg19/b37 flexibility was being applied to VCF datasources and inducing a lot of missed annotations.
    - Sanitizing funcotations in VCF.
    - Implemented lookahead caching and merged with master.
    - Added Funcotator test for clinvar and Gencode v28 in hg38
    - Added funcotator test to make sure that mixed chr/no-chr GENCODE and datasources would still annotate properly for hg19.
    - Eased restrictions so that Gencode v28 would be recognized as a valid gtf
    - Added warning so that future versions of Gencode would not fail just based on the version number and warning would be emitted instead (@jonn-smith)
    - Altered the lookahead default value to specific for backend.
    LeeTL1220 committed May 22, 2018
    Configuration menu
    Copy the full SHA
    7602872 View commit details
    Browse the repository at this point in the history
  2. Responding to PR comments

    LeeTL1220 committed May 22, 2018
    Configuration menu
    Copy the full SHA
    338b70d View commit details
    Browse the repository at this point in the history
  3. Configuration menu
    Copy the full SHA
    6876fd8 View commit details
    Browse the repository at this point in the history

Commits on May 23, 2018

  1. - Tarring other test references.

    - Created a class to minimize the number of copies we make of each untarred test reference.
    LeeTL1220 committed May 23, 2018
    Configuration menu
    Copy the full SHA
    a315df8 View commit details
    Browse the repository at this point in the history
  2. Configuration menu
    Copy the full SHA
    2199d85 View commit details
    Browse the repository at this point in the history
  3. Additional small fixes.

    LeeTL1220 committed May 23, 2018
    Configuration menu
    Copy the full SHA
    8ad6c53 View commit details
    Browse the repository at this point in the history
  4. WDL fix.

    LeeTL1220 committed May 23, 2018
    Configuration menu
    Copy the full SHA
    d6927b6 View commit details
    Browse the repository at this point in the history

Commits on May 24, 2018

  1. Configuration menu
    Copy the full SHA
    1e8a010 View commit details
    Browse the repository at this point in the history