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

VCF 4.5 Future of VCF scaling improvements #758

Merged
merged 14 commits into from
Apr 20, 2024
Merged

VCF 4.5 Future of VCF scaling improvements #758

merged 14 commits into from
Apr 20, 2024

Commits on Feb 27, 2024

  1. Rebased #434 onto VCFv4.5

    Daniel Cameron committed Feb 27, 2024
    Configuration menu
    Copy the full SHA
    9d72212 View commit details
    Browse the repository at this point in the history

  2. Redefined LAA to require explicit inclusion of 0 for REF; require LGT… 

    … to be before other fields
    Daniel Cameron committed Feb 27, 2024
    Configuration menu
    Copy the full SHA
    35894af View commit details
    Browse the repository at this point in the history

  3. Added FORMAT END to support sample-specific $<$*$>$ alleles (alternat… 

    …ive to #435)
    Daniel Cameron committed Feb 27, 2024
    Configuration menu
    Copy the full SHA
    4ebc5aa View commit details
    Browse the repository at this point in the history

  4. Fixed typo 

    Co-authored-by: John Marshall <jmarshall@hey.com>
    @d-cameron @jmarshall
    d-cameron and jmarshall committed Feb 27, 2024
    Configuration menu
    Copy the full SHA
    099fe19 View commit details
    Browse the repository at this point in the history

Commits on Apr 20, 2024

  1. Updated examples from LAA notation to LA 

    Co-authored-by: Dan King <daniel.zidan.king@gmail.com>
    @d-cameron @danking
    d-cameron and danking committed Apr 20, 2024
    Configuration menu
    Copy the full SHA
    9b472b4 View commit details
    Browse the repository at this point in the history

  2. Renamed LAA to LA to reflect inclusion of reference allele

    @d-cameron
    d-cameron committed Apr 20, 2024
    Configuration menu
    Copy the full SHA
    00b01f3 View commit details
    Browse the repository at this point in the history

  3. Using FORMAT LEN and deprecating INFO END

    @d-cameron
    d-cameron committed Apr 20, 2024
    Configuration menu
    Copy the full SHA
    197d3b3 View commit details
    Browse the repository at this point in the history

  4. Added Number=LOCAL-A, LOCAL-R, LOCAL-G, P

    @d-cameron
    d-cameron committed Apr 20, 2024
    Configuration menu
    Copy the full SHA
    46e4f9f View commit details
    Browse the repository at this point in the history

  5. Clarified what happens when and field and it's local-allele are both … 

    …present
    @d-cameron
    d-cameron committed Apr 20, 2024
    Configuration menu
    Copy the full SHA
    d769847 View commit details
    Browse the repository at this point in the history

  6. Using less verbose LA instead of LOCAL-A

    @d-cameron
    d-cameron committed Apr 20, 2024
    Configuration menu
    Copy the full SHA
    abf2531 View commit details
    Browse the repository at this point in the history

  7. Removed ordering requirement on LA. REF=0 must still be the first entry

    @d-cameron
    d-cameron committed Apr 20, 2024
    Configuration menu
    Copy the full SHA
    be3b990 View commit details
    Browse the repository at this point in the history

  8. Made GT/LGT consistency requirement explicit; fixed typos

    @d-cameron
    d-cameron committed Apr 20, 2024
    Configuration menu
    Copy the full SHA
    7e0db98 View commit details
    Browse the repository at this point in the history

  9. LA->LAA. Clarified ambiguities introduced. Added test case.

    @d-cameron
    d-cameron committed Apr 20, 2024
    Configuration menu
    Copy the full SHA
    26a9326 View commit details
    Browse the repository at this point in the history

  10. Made 1-based LAA explicit in multiple places. Fixed typos

    @d-cameron
    d-cameron committed Apr 20, 2024
    Configuration menu
    Copy the full SHA
    3e73e10 View commit details
    Browse the repository at this point in the history