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

Reorganized files #34

Open
wants to merge 23 commits into
base: master
Choose a base branch
from
Open

Reorganized files #34

wants to merge 23 commits into from

Commits on May 15, 2024

  1. test

    @jimmy-penn
    jimmy-penn committed May 15, 2024
    Configuration menu
    Copy the full SHA
    d2e1d7d View commit details
    Browse the repository at this point in the history

  2. Reorganize files

    @jimmy-penn
    jimmy-penn committed May 15, 2024
    Configuration menu
    Copy the full SHA
    5fa528d View commit details
    Browse the repository at this point in the history

  3. Add medium testing

    @jimmy-penn
    jimmy-penn committed May 15, 2024
    Configuration menu
    Copy the full SHA
    4d4cbf6 View commit details
    Browse the repository at this point in the history

Commits on May 21, 2024

  1. Minor changes

    @jimmy-penn
    jimmy-penn committed May 21, 2024
    Configuration menu
    Copy the full SHA
    1e9704f View commit details
    Browse the repository at this point in the history

  2. Add functions to read AFs from subpopulations

    @jimmy-penn
    jimmy-penn committed May 21, 2024
    Configuration menu
    Copy the full SHA
    3c87009 View commit details
    Browse the repository at this point in the history

Commits on May 23, 2024

  1. Add functions to calculate additional scores for subcontinental popul… 

    …ations
    @jimmy-penn
    jimmy-penn committed May 23, 2024
    Configuration menu
    Copy the full SHA
    ecbd0c5 View commit details
    Browse the repository at this point in the history

Commits on May 31, 2024

  1. Add code to calculate scores for clustering African subpopulations.

    @jimmy-penn
    jimmy-penn committed May 31, 2024
    Configuration menu
    Copy the full SHA
    19a7aa2 View commit details
    Browse the repository at this point in the history

Commits on Jun 13, 2024

  1. Normalized newly added scores for clustering subcontinental populations.

    @jimmy-penn
    jimmy-penn committed Jun 13, 2024
    Configuration menu
    Copy the full SHA
    23ff431 View commit details
    Browse the repository at this point in the history

Commits on Jun 14, 2024

  1. Added code to save and display raw subcontinental population scores.

    @jimmy-penn
    jimmy-penn committed Jun 14, 2024
    Configuration menu
    Copy the full SHA
    e849c17 View commit details
    Browse the repository at this point in the history

Commits on Jun 21, 2024

  1. Fixed a bug. Removed GD4 and replaced it with a normalized score GL1.… 

    … Replaced EU3 with GL2.
    @jimmy-penn
    jimmy-penn committed Jun 21, 2024
    Configuration menu
    Copy the full SHA
    a2c58e0 View commit details
    Browse the repository at this point in the history

Commits on Aug 27, 2024

  1. Modified code to take new list of global level reference populations

    @jimmy-penn
    jimmy-penn committed Aug 27, 2024
    Configuration menu
    Copy the full SHA
    0d51447 View commit details
    Browse the repository at this point in the history

Commits on Sep 5, 2024

  1. Added code to calculate scores for EA subpopulations

    @jimmy-penn
    jimmy-penn committed Sep 5, 2024
    Configuration menu
    Copy the full SHA
    9a6058b View commit details
    Browse the repository at this point in the history

Commits on Oct 8, 2024

  1. Modified code to save memory space. Fixed a bug with duplicated SNP IDs.

    @jimmy-penn
    jimmy-penn committed Oct 8, 2024
    Configuration menu
    Copy the full SHA
    d7db376 View commit details
    Browse the repository at this point in the history

  2. Code to check format of ancestry SNP file

    @jimmy-penn
    jimmy-penn committed Oct 8, 2024
    Configuration menu
    Copy the full SHA
    7db1a77 View commit details
    Browse the repository at this point in the history

  3. Some minor changes

    @jimmy-penn
    jimmy-penn committed Oct 8, 2024
    Configuration menu
    Copy the full SHA
    46c524d View commit details
    Browse the repository at this point in the history

Commits on Nov 11, 2024

  1. Swithed EA1 and EA3

    @jimmy-penn
    jimmy-penn committed Nov 11, 2024
    Configuration menu
    Copy the full SHA
    fb38bf9 View commit details
    Browse the repository at this point in the history

Commits on Nov 18, 2024

  1. Reimplement vcf parser using htslib

    @jimmy-penn
    jimmy-penn committed Nov 18, 2024
    Configuration menu
    Copy the full SHA
    96b17b2 View commit details
    Browse the repository at this point in the history

Commits on Nov 19, 2024

  1. Modified PLINK parser to allow reading a chunk of samples

    @jimmy-penn
    jimmy-penn committed Nov 19, 2024
    Configuration menu
    Copy the full SHA
    346c79b View commit details
    Browse the repository at this point in the history

Commits on Nov 21, 2024

  1. Optimize memory use for both VCF and PLINK input

    @jimmy-penn
    jimmy-penn committed Nov 21, 2024
    Configuration menu
    Copy the full SHA
    0acdea6 View commit details
    Browse the repository at this point in the history

  2. Bug fixes and minor improvements

    @jimmy-penn
    jimmy-penn committed Nov 21, 2024
    Configuration menu
    Copy the full SHA
    da47fd4 View commit details
    Browse the repository at this point in the history

Commits on Nov 22, 2024

  1. Add code to calculate heterozy rate for each sample

    @jimmy-penn
    jimmy-penn committed Nov 22, 2024
    Configuration menu
    Copy the full SHA
    65d4165 View commit details
    Browse the repository at this point in the history

Commits on Nov 26, 2024

  1. Added raw Pe, Pf, Pa scores

    @jimmy-penn
    jimmy-penn committed Nov 26, 2024
    Configuration menu
    Copy the full SHA
    64752e2 View commit details
    Browse the repository at this point in the history

Commits on Nov 27, 2024

  1. Add code to take user-specified memory size, sample block size, threads

    @jimmy-penn
    jimmy-penn committed Nov 27, 2024
    Configuration menu
    Copy the full SHA
    a19910a View commit details
    Browse the repository at this point in the history