Fix memory issues for larger sample sizes #271

jaamarks · 2024-03-25T16:15:29Z

Fixes #241 . Make changes to handle larger sample sizes.

change some resource parameters,
switch some local rules to jobs submitted to cluster,
adjust time allocation formatting for compatibility with the Slurm scheduler to accept durations exceeding 24 hours,
increase ibd_min_pi_hat parameter from 0.05 to 0.12 with corresponding updates to unit tests,
and fix minor bugs.

…mple sizes.

… 3rd-degree)

…sues.

jaamarks added 10 commits March 21, 2024 12:33

fix spacing issues per PEP 8 other recommendations

773eb1f

format time for slurm

af39a8d

Make plink and sample_qc rules more scalable to accommodate larger sa…

1e04775

…mple sizes.

Fixes #265: tim_hr -> time_hr

3d49259

Increase ibd_pi_hat_min to 0.12 to focus on closer relatives (roughly…

bd74c72

… 3rd-degree)

Improve memory & time handling for larger datasets. Fix formatting is…

c6efdd3

…sues.

focus on 3rd-degree and up

e3733f7

remove copy of init and fix typo

b7bd763

apply black formatting suggestions

4d2a3d1

update repo in pyproject.toml from old gitlab to current github

b9c29cd

jaamarks merged commit 458b6bb into default Apr 1, 2024
2 checks passed

jaamarks deleted the memory-issue-241 branch April 12, 2024 14:03

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