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

Feature/chunked writer precomputed burdens testing combo #135

Merged
merged 141 commits into from
Sep 24, 2024
Merged

Feature/chunked writer precomputed burdens testing combo #135

merged 141 commits into from
Sep 24, 2024

Commits on Mar 4, 2024

  1. make genotype and variant files optional

    @bfclarke
    bfclarke committed Mar 4, 2024
    Configuration menu
    Copy the full SHA
    2e4ea84 View commit details
    Browse the repository at this point in the history

  2. specify burden file manually

    @bfclarke
    bfclarke committed Mar 4, 2024
    Configuration menu
    Copy the full SHA
    94722ed View commit details
    Browse the repository at this point in the history

Commits on Mar 5, 2024

  1. specify burden file manually

    @bfclarke
    bfclarke committed Mar 5, 2024
    Configuration menu
    Copy the full SHA
    5655919 View commit details
    Browse the repository at this point in the history

Commits on Mar 12, 2024

  1. add pipelines

    @bfclarke
    bfclarke committed Mar 12, 2024
    Configuration menu
    Copy the full SHA
    742b09f View commit details
    Browse the repository at this point in the history

  2. bug fixes

    @bfclarke
    bfclarke committed Mar 12, 2024
    Configuration menu
    Copy the full SHA
    8deacd9 View commit details
    Browse the repository at this point in the history

  3. add pipelines

    @bfclarke
    bfclarke committed Mar 12, 2024
    Configuration menu
    Copy the full SHA
    ad61bd4 View commit details
    Browse the repository at this point in the history

  4. add eval pipeline

    @bfclarke
    bfclarke committed Mar 12, 2024
    Configuration menu
    Copy the full SHA
    3801859 View commit details
    Browse the repository at this point in the history

Commits on Mar 15, 2024

  1. Small bug fix removing overwriting of function option name.

    @ThibaultBechtler
    ThibaultBechtler committed Mar 15, 2024
    Configuration menu
    Copy the full SHA
    1f8c424 View commit details
    Browse the repository at this point in the history

Commits on Mar 29, 2024

  1. add argument for additional REGENIE options

    @bfclarke
    bfclarke committed Mar 29, 2024
    Configuration menu
    Copy the full SHA
    48b039f View commit details
    Browse the repository at this point in the history

  2. keep beta in results

    @bfclarke
    bfclarke committed Mar 29, 2024
    Configuration menu
    Copy the full SHA
    4c45063 View commit details
    Browse the repository at this point in the history

  3. add conditional analysis

    @bfclarke
    bfclarke committed Mar 29, 2024
    Configuration menu
    Copy the full SHA
    7925630 View commit details
    Browse the repository at this point in the history

  4. Merge branch 'feature-precomputed-burden-testing' of github.com:PMBio… 

    …/deeprvat into feature-precomputed-burden-testing
    @bfclarke
    bfclarke committed Mar 29, 2024
    Configuration menu
    Copy the full SHA
    67fa91c View commit details
    Browse the repository at this point in the history

Commits on Apr 11, 2024

  1. run regenie_step2 in long queue

    @bfclarke
    bfclarke committed Apr 11, 2024
    Configuration menu
    Copy the full SHA
    b964fda View commit details
    Browse the repository at this point in the history

  2. improve modularity

    @bfclarke
    bfclarke committed Apr 11, 2024
    Configuration menu
    Copy the full SHA
    dd41088 View commit details
    Browse the repository at this point in the history

Commits on Apr 12, 2024

  1. remove .loco files from output/input

    @bfclarke
    bfclarke committed Apr 12, 2024
    Configuration menu
    Copy the full SHA
    f9e8698 View commit details
    Browse the repository at this point in the history

Commits on Apr 17, 2024

  1. run REGENIE step 2 on verylong queue

    @bfclarke
    bfclarke committed Apr 17, 2024
    Configuration menu
    Copy the full SHA
    232fd72 View commit details
    Browse the repository at this point in the history

  2. bug fixes

    @bfclarke
    bfclarke committed Apr 17, 2024
    Configuration menu
    Copy the full SHA
    b539cd3 View commit details
    Browse the repository at this point in the history

Commits on Apr 30, 2024

  1. bug fixes

    @bfclarke
    bfclarke committed Apr 30, 2024
    Configuration menu
    Copy the full SHA
    4dca15d View commit details
    Browse the repository at this point in the history

Commits on May 7, 2024

  1. Add tests

    @endast
    endast committed May 7, 2024
    Configuration menu
    Copy the full SHA
    c28b69d View commit details
    Browse the repository at this point in the history

  2. Add test data for merging

    @endast
    endast committed May 7, 2024
    Configuration menu
    Copy the full SHA
    9c718f7 View commit details
    Browse the repository at this point in the history

  3. Fix test path

    @endast
    endast committed May 7, 2024
    Configuration menu
    Copy the full SHA
    2ceabb5 View commit details
    Browse the repository at this point in the history

  4. unused variable

    @endast
    endast committed May 7, 2024
    Configuration menu
    Copy the full SHA
    28798ac View commit details
    Browse the repository at this point in the history

  5. Merge branch 'feature-precomputed-burden-testing' into feature/chunke… 

    …d-writer-precompyted-burdens-testing
    @endast
    endast committed May 7, 2024
    Configuration menu
    Copy the full SHA
    69e20e0 View commit details
    Browse the repository at this point in the history

Commits on May 15, 2024

  1. bug fix

    @bfclarke
    bfclarke committed May 15, 2024
    Configuration menu
    Copy the full SHA
    0a25ffd View commit details
    Browse the repository at this point in the history

Commits on May 17, 2024

  1. bug fix (remove broken debugging code)

    @bfclarke
    bfclarke committed May 17, 2024
    Configuration menu
    Copy the full SHA
    ccb92c1 View commit details
    Browse the repository at this point in the history

  2. remove duplicate rule

    @bfclarke
    bfclarke committed May 17, 2024
    Configuration menu
    Copy the full SHA
    669140b View commit details
    Browse the repository at this point in the history

Commits on May 22, 2024

  1. update pipelines for new burden directory structure

    @bfclarke
    bfclarke committed May 22, 2024
    Configuration menu
    Copy the full SHA
    7d13b7b View commit details
    Browse the repository at this point in the history

  2. bug fixes for REGENIE pipeline

    @bfclarke
    bfclarke committed May 22, 2024
    Configuration menu
    Copy the full SHA
    751c23d View commit details
    Browse the repository at this point in the history

  3. bug fixes for REGENIE pipelines

    @bfclarke
    bfclarke committed May 22, 2024
    Configuration menu
    Copy the full SHA
    97b43ec View commit details
    Browse the repository at this point in the history

Commits on May 23, 2024

  1. add option for determinism in training

    @bfclarke
    bfclarke committed May 23, 2024
    Configuration menu
    Copy the full SHA
    cbd4dcf View commit details
    Browse the repository at this point in the history

Commits on Jun 25, 2024

  1. add test for results of training_association_testing pipeline

    @bfclarke
    bfclarke committed Jun 25, 2024
    Configuration menu
    Copy the full SHA
    4b48b0e View commit details
    Browse the repository at this point in the history

Commits on Jul 1, 2024

  1. make genotype and variant files optional

    @bfclarke
    bfclarke committed Jul 1, 2024
    Configuration menu
    Copy the full SHA
    c6b4f3b View commit details
    Browse the repository at this point in the history

  2. specify burden file manually

    @bfclarke
    bfclarke committed Jul 1, 2024
    Configuration menu
    Copy the full SHA
    7bcae5f View commit details
    Browse the repository at this point in the history

  3. specify burden file manually

    @bfclarke
    bfclarke committed Jul 1, 2024
    Configuration menu
    Copy the full SHA
    9b9c6e5 View commit details
    Browse the repository at this point in the history

  4. add pipelines

    @bfclarke
    bfclarke committed Jul 1, 2024
    Configuration menu
    Copy the full SHA
    ca26206 View commit details
    Browse the repository at this point in the history

  5. bug fixes

    @bfclarke
    bfclarke committed Jul 1, 2024
    Configuration menu
    Copy the full SHA
    a51d40e View commit details
    Browse the repository at this point in the history

  6. add pipelines

    @bfclarke
    bfclarke committed Jul 1, 2024
    Configuration menu
    Copy the full SHA
    d76628f View commit details
    Browse the repository at this point in the history

  7. add eval pipeline

    @bfclarke
    bfclarke committed Jul 1, 2024
    Configuration menu
    Copy the full SHA
    0bc1409 View commit details
    Browse the repository at this point in the history

  8. add argument for additional REGENIE options

    @bfclarke
    bfclarke committed Jul 1, 2024
    Configuration menu
    Copy the full SHA
    b0940e9 View commit details
    Browse the repository at this point in the history

  9. add conditional analysis

    @bfclarke
    bfclarke committed Jul 1, 2024
    Configuration menu
    Copy the full SHA
    318c793 View commit details
    Browse the repository at this point in the history

  10. Small bug fix removing overwriting of function option name.

    @ThibaultBechtler @bfclarke
    ThibaultBechtler authored and bfclarke committed Jul 1, 2024
    Configuration menu
    Copy the full SHA
    1a765b0 View commit details
    Browse the repository at this point in the history

  11. run regenie_step2 in long queue

    @bfclarke
    bfclarke committed Jul 1, 2024
    Configuration menu
    Copy the full SHA
    48900ea View commit details
    Browse the repository at this point in the history

  12. improve modularity

    @bfclarke
    bfclarke committed Jul 1, 2024
    Configuration menu
    Copy the full SHA
    a03e0ee View commit details
    Browse the repository at this point in the history

  13. remove .loco files from output/input

    @bfclarke
    bfclarke committed Jul 1, 2024
    Configuration menu
    Copy the full SHA
    2380406 View commit details
    Browse the repository at this point in the history

  14. run REGENIE step 2 on verylong queue

    @bfclarke
    bfclarke committed Jul 1, 2024
    Configuration menu
    Copy the full SHA
    d810e41 View commit details
    Browse the repository at this point in the history

  15. bug fixes

    @bfclarke
    bfclarke committed Jul 1, 2024
    Configuration menu
    Copy the full SHA
    e69b33c View commit details
    Browse the repository at this point in the history

  16. bug fixes

    @bfclarke
    bfclarke committed Jul 1, 2024
    Configuration menu
    Copy the full SHA
    756d797 View commit details
    Browse the repository at this point in the history

  17. bug fix

    @bfclarke
    bfclarke committed Jul 1, 2024
    Configuration menu
    Copy the full SHA
    6965d73 View commit details
    Browse the repository at this point in the history

  18. bug fix (remove broken debugging code)

    @bfclarke
    bfclarke committed Jul 1, 2024
    Configuration menu
    Copy the full SHA
    50ed569 View commit details
    Browse the repository at this point in the history

  19. remove duplicate rule

    @bfclarke
    bfclarke committed Jul 1, 2024
    Configuration menu
    Copy the full SHA
    d041c64 View commit details
    Browse the repository at this point in the history

Commits on Jul 3, 2024

  1. update pipelines for new burden directory structure

    @bfclarke
    bfclarke committed Jul 3, 2024
    Configuration menu
    Copy the full SHA
    32ba53f View commit details
    Browse the repository at this point in the history

  2. bug fixes for REGENIE pipeline

    @bfclarke
    bfclarke committed Jul 3, 2024
    Configuration menu
    Copy the full SHA
    213d184 View commit details
    Browse the repository at this point in the history

  3. bug fixes for REGENIE pipelines

    @bfclarke
    bfclarke committed Jul 3, 2024
    Configuration menu
    Copy the full SHA
    34a4608 View commit details
    Browse the repository at this point in the history

  4. add option for determinism in training

    @bfclarke
    bfclarke committed Jul 3, 2024
    Configuration menu
    Copy the full SHA
    01e1e42 View commit details
    Browse the repository at this point in the history

  5. add test for results of training_association_testing pipeline

    @bfclarke
    bfclarke committed Jul 3, 2024
    Configuration menu
    Copy the full SHA
    6d19c0d View commit details
    Browse the repository at this point in the history

  6. Merge branch 'feature-precomputed-burden-testing' of github.com:PMBio… 

    …/deeprvat into feature-precomputed-burden-testing
    @bfclarke
    bfclarke committed Jul 3, 2024
    Configuration menu
    Copy the full SHA
    218200d View commit details
    Browse the repository at this point in the history

Commits on Aug 22, 2024

  1. make genotype and variant files optional

    @bfclarke
    bfclarke committed Aug 22, 2024
    Configuration menu
    Copy the full SHA
    4ce40b2 View commit details
    Browse the repository at this point in the history

  2. specify burden file manually

    @bfclarke
    bfclarke committed Aug 22, 2024
    Configuration menu
    Copy the full SHA
    2edde91 View commit details
    Browse the repository at this point in the history

  3. specify burden file manually

    @bfclarke
    bfclarke committed Aug 22, 2024
    Configuration menu
    Copy the full SHA
    d4f929e View commit details
    Browse the repository at this point in the history

  4. add pipelines

    @bfclarke
    bfclarke committed Aug 22, 2024
    Configuration menu
    Copy the full SHA
    9124ea7 View commit details
    Browse the repository at this point in the history

  5. bug fixes

    @bfclarke
    bfclarke committed Aug 22, 2024
    Configuration menu
    Copy the full SHA
    878b322 View commit details
    Browse the repository at this point in the history

  6. add pipelines

    @bfclarke
    bfclarke committed Aug 22, 2024
    Configuration menu
    Copy the full SHA
    e14fc85 View commit details
    Browse the repository at this point in the history

  7. add eval pipeline

    @bfclarke
    bfclarke committed Aug 22, 2024
    Configuration menu
    Copy the full SHA
    abbd76b View commit details
    Browse the repository at this point in the history

  8. add argument for additional REGENIE options

    @bfclarke
    bfclarke committed Aug 22, 2024
    Configuration menu
    Copy the full SHA
    801fff8 View commit details
    Browse the repository at this point in the history

  9. add conditional analysis

    @bfclarke
    bfclarke committed Aug 22, 2024
    Configuration menu
    Copy the full SHA
    e83cd7c View commit details
    Browse the repository at this point in the history

  10. Small bug fix removing overwriting of function option name.

    @ThibaultBechtler @bfclarke
    ThibaultBechtler authored and bfclarke committed Aug 22, 2024
    Configuration menu
    Copy the full SHA
    0e33290 View commit details
    Browse the repository at this point in the history

  11. run regenie_step2 in long queue

    @bfclarke
    bfclarke committed Aug 22, 2024
    Configuration menu
    Copy the full SHA
    585e399 View commit details
    Browse the repository at this point in the history

  12. improve modularity

    @bfclarke
    bfclarke committed Aug 22, 2024
    Configuration menu
    Copy the full SHA
    14990b9 View commit details
    Browse the repository at this point in the history

  13. remove .loco files from output/input

    @bfclarke
    bfclarke committed Aug 22, 2024
    Configuration menu
    Copy the full SHA
    b2d292c View commit details
    Browse the repository at this point in the history

  14. run REGENIE step 2 on verylong queue

    @bfclarke
    bfclarke committed Aug 22, 2024
    Configuration menu
    Copy the full SHA
    a9cc677 View commit details
    Browse the repository at this point in the history

  15. bug fixes

    @bfclarke
    bfclarke committed Aug 22, 2024
    Configuration menu
    Copy the full SHA
    d2ae3b7 View commit details
    Browse the repository at this point in the history

  16. bug fixes

    @bfclarke
    bfclarke committed Aug 22, 2024
    Configuration menu
    Copy the full SHA
    3f9beaa View commit details
    Browse the repository at this point in the history

  17. bug fix

    @bfclarke
    bfclarke committed Aug 22, 2024
    Configuration menu
    Copy the full SHA
    c7e8bd0 View commit details
    Browse the repository at this point in the history

  18. bug fix (remove broken debugging code)

    @bfclarke
    bfclarke committed Aug 22, 2024
    Configuration menu
    Copy the full SHA
    f297ff8 View commit details
    Browse the repository at this point in the history

  19. remove duplicate rule

    @bfclarke
    bfclarke committed Aug 22, 2024
    Configuration menu
    Copy the full SHA
    07661ec View commit details
    Browse the repository at this point in the history

  20. update pipelines for new burden directory structure

    @bfclarke
    bfclarke committed Aug 22, 2024
    Configuration menu
    Copy the full SHA
    9c8fbde View commit details
    Browse the repository at this point in the history

  21. bug fixes for REGENIE pipeline

    @bfclarke
    bfclarke committed Aug 22, 2024
    Configuration menu
    Copy the full SHA
    4f1f1fa View commit details
    Browse the repository at this point in the history

  22. bug fixes for REGENIE pipelines

    @bfclarke
    bfclarke committed Aug 22, 2024
    Configuration menu
    Copy the full SHA
    3bc2fb0 View commit details
    Browse the repository at this point in the history

  23. add option for determinism in training

    @bfclarke
    bfclarke committed Aug 22, 2024
    Configuration menu
    Copy the full SHA
    e55c902 View commit details
    Browse the repository at this point in the history

  24. add test for results of training_association_testing pipeline

    @bfclarke
    bfclarke committed Aug 22, 2024
    Configuration menu
    Copy the full SHA
    010c22c View commit details
    Browse the repository at this point in the history

  25. make genotype and variant files optional

    @bfclarke
    bfclarke committed Aug 22, 2024
    Configuration menu
    Copy the full SHA
    90c65a7 View commit details
    Browse the repository at this point in the history

  26. specify burden file manually

    @bfclarke
    bfclarke committed Aug 22, 2024
    Configuration menu
    Copy the full SHA
    e1992c7 View commit details
    Browse the repository at this point in the history

  27. specify burden file manually

    @bfclarke
    bfclarke committed Aug 22, 2024
    Configuration menu
    Copy the full SHA
    f7bc9c0 View commit details
    Browse the repository at this point in the history

  28. bug fixes

    @bfclarke
    bfclarke committed Aug 22, 2024
    Configuration menu
    Copy the full SHA
    b5fdf0a View commit details
    Browse the repository at this point in the history

  29. add eval pipeline

    @bfclarke
    bfclarke committed Aug 22, 2024
    Configuration menu
    Copy the full SHA
    0d1da22 View commit details
    Browse the repository at this point in the history

  30. add argument for additional REGENIE options

    @bfclarke
    bfclarke committed Aug 22, 2024
    Configuration menu
    Copy the full SHA
    b6a5b4b View commit details
    Browse the repository at this point in the history

Commits on Aug 23, 2024

  1. update pipelines for new burden directory structure

    @bfclarke
    bfclarke committed Aug 23, 2024
    Configuration menu
    Copy the full SHA
    232e7dd View commit details
    Browse the repository at this point in the history

  2. bug fixes for REGENIE pipelines

    @bfclarke
    bfclarke committed Aug 23, 2024
    Configuration menu
    Copy the full SHA
    28b616e View commit details
    Browse the repository at this point in the history

  3. add test for results of training_association_testing pipeline

    @bfclarke
    bfclarke committed Aug 23, 2024
    Configuration menu
    Copy the full SHA
    686e5d3 View commit details
    Browse the repository at this point in the history

  4. corrections to pipelines

    @bfclarke
    bfclarke committed Aug 23, 2024
    Configuration menu
    Copy the full SHA
    8d99a4d View commit details
    Browse the repository at this point in the history

  5. Merge branch 'feature-precomputed-burden-testing' of github.com:PMBio… 

    …/deeprvat into feature-precomputed-burden-testing
    @bfclarke
    bfclarke committed Aug 23, 2024
    Configuration menu
    Copy the full SHA
    f35fe30 View commit details
    Browse the repository at this point in the history

Commits on Aug 27, 2024

  1. delete old example config

    @bfclarke
    bfclarke committed Aug 27, 2024
    Configuration menu
    Copy the full SHA
    f57b29e View commit details
    Browse the repository at this point in the history

Commits on Aug 28, 2024

  1. bug fixes for new config file naming

    @bfclarke
    bfclarke committed Aug 28, 2024
    Configuration menu
    Copy the full SHA
    43255d0 View commit details
    Browse the repository at this point in the history

  2. improve error message when repo is misspecified

    @bfclarke
    bfclarke committed Aug 28, 2024
    Configuration menu
    Copy the full SHA
    4347fd1 View commit details
    Browse the repository at this point in the history

  3. correct data key

    @bfclarke
    bfclarke committed Aug 28, 2024
    Configuration menu
    Copy the full SHA
    da0474c View commit details
    Browse the repository at this point in the history

  4. add command to compare association testing results

    @bfclarke
    bfclarke committed Aug 28, 2024
    Configuration menu
    Copy the full SHA
    b86ff09 View commit details
    Browse the repository at this point in the history

  5. cast trial ID to int to fix intermittent bug where it's stored as float

    @bfclarke
    bfclarke committed Aug 28, 2024
    Configuration menu
    Copy the full SHA
    703c27c View commit details
    Browse the repository at this point in the history

  6. expose deterministic option (for testing/debugging)

    @bfclarke
    bfclarke committed Aug 28, 2024
    Configuration menu
    Copy the full SHA
    d2d59d4 View commit details
    Browse the repository at this point in the history

Commits on Aug 30, 2024

  1. Merge branch 'feature-precomputed-burden-testing' into feature/chunke… 

    …d-writer-precompyted-burdens-testing
    @endast
    endast committed Aug 30, 2024
    Configuration menu
    Copy the full SHA
    54ef3b3 View commit details
    Browse the repository at this point in the history

Commits on Sep 3, 2024

  1. Add initial changes

    @endast
    endast committed Sep 3, 2024
    Configuration menu
    Copy the full SHA
    d700de4 View commit details
    Browse the repository at this point in the history

  2. remove deeprvat_repo_dir

    @endast
    endast committed Sep 3, 2024
    Configuration menu
    Copy the full SHA
    d26b548 View commit details
    Browse the repository at this point in the history

  3. Add chunked writer

    @endast
    endast committed Sep 3, 2024
    Configuration menu
    Copy the full SHA
    32f409d View commit details
    Browse the repository at this point in the history

  4. Remove deeprvat from paths

    @endast
    endast committed Sep 3, 2024
    Configuration menu
    Copy the full SHA
    c470c84 View commit details
    Browse the repository at this point in the history

Commits on Sep 4, 2024

  1. Fix dtype

    @endast
    endast committed Sep 4, 2024
    Configuration menu
    Copy the full SHA
    739717e View commit details
    Browse the repository at this point in the history

  2. Add merge to snakemake pipeline

    @endast
    endast committed Sep 4, 2024
    Configuration menu
    Copy the full SHA
    c77d793 View commit details
    Browse the repository at this point in the history

  3. Remove x.zarr and y.zarr

    @endast
    endast committed Sep 4, 2024
    Configuration menu
    Copy the full SHA
    c891b41 View commit details
    Browse the repository at this point in the history

  4. Working test for 5 chunks

    @endast
    endast committed Sep 4, 2024
    Configuration menu
    Copy the full SHA
    06e34b6 View commit details
    Browse the repository at this point in the history

  5. Add back sample_ids test

    @endast
    endast committed Sep 4, 2024
    Configuration menu
    Copy the full SHA
    3ad8434 View commit details
    Browse the repository at this point in the history

  6. Fix pretrained path

    @endast
    endast committed Sep 4, 2024
    Configuration menu
    Copy the full SHA
    45f6a32 View commit details
    Browse the repository at this point in the history

  7. Remove phenotypes key

    @endast
    endast committed Sep 4, 2024
    Configuration menu
    Copy the full SHA
    dd62d49 View commit details
    Browse the repository at this point in the history

  8. Merge branch 'feature/chunked-writer-precomputed-burdens-testing-comb… 

    …o' of github.com:PMBio/deeprvat into feature/chunked-writer-precomputed-burdens-testing-combo
    @endast
    endast committed Sep 4, 2024
    Configuration menu
    Copy the full SHA
    7873bac View commit details
    Browse the repository at this point in the history

  9. Fix failing tests

    @endast
    endast committed Sep 4, 2024
    Configuration menu
    Copy the full SHA
    db92c10 View commit details
    Browse the repository at this point in the history

  10. More config errors

    @endast
    endast committed Sep 4, 2024
    Configuration menu
    Copy the full SHA
    ff82d44 View commit details
    Browse the repository at this point in the history

Commits on Sep 9, 2024

  1. fixes to pipelines

    @bfclarke
    bfclarke committed Sep 9, 2024
    Configuration menu
    Copy the full SHA
    0b6aeda View commit details
    Browse the repository at this point in the history

  2. remove unfinished sections

    @bfclarke
    bfclarke committed Sep 9, 2024
    Configuration menu
    Copy the full SHA
    6c6bf2f View commit details
    Browse the repository at this point in the history

Commits on Sep 10, 2024

  1. pipeline fixes

    @bfclarke
    bfclarke committed Sep 10, 2024
    Configuration menu
    Copy the full SHA
    5181ed6 View commit details
    Browse the repository at this point in the history

  2. reduce number of phenotypes in example configs

    @bfclarke
    bfclarke committed Sep 10, 2024
    Configuration menu
    Copy the full SHA
    68d2ccd View commit details
    Browse the repository at this point in the history

  3. bug fix

    @bfclarke
    bfclarke committed Sep 10, 2024
    Configuration menu
    Copy the full SHA
    0c70898 View commit details
    Browse the repository at this point in the history

  4. pipeline fixes

    @bfclarke
    bfclarke committed Sep 10, 2024
    Configuration menu
    Copy the full SHA
    5511a6d View commit details
    Browse the repository at this point in the history

  5. add example config for REGENIE

    @bfclarke
    bfclarke committed Sep 10, 2024
    Configuration menu
    Copy the full SHA
    4dace76 View commit details
    Browse the repository at this point in the history

  6. pipeline fixes

    @bfclarke
    bfclarke committed Sep 10, 2024
    Configuration menu
    Copy the full SHA
    49979ab View commit details
    Browse the repository at this point in the history

  7. pipeline fixes

    @bfclarke
    bfclarke committed Sep 10, 2024
    Configuration menu
    Copy the full SHA
    e41bb3a View commit details
    Browse the repository at this point in the history

  8. pipeline fixes

    @bfclarke
    bfclarke committed Sep 10, 2024
    Configuration menu
    Copy the full SHA
    dc5df06 View commit details
    Browse the repository at this point in the history

Commits on Sep 13, 2024

  1. adapt CV pipeline

    @bfclarke
    bfclarke committed Sep 13, 2024
    Configuration menu
    Copy the full SHA
    ebd7baf View commit details
    Browse the repository at this point in the history

Commits on Sep 16, 2024

  1. pipeline fix

    @bfclarke
    bfclarke committed Sep 16, 2024
    Configuration menu
    Copy the full SHA
    52b3990 View commit details
    Browse the repository at this point in the history

Commits on Sep 17, 2024

  1. reduce uninformative logging

    @bfclarke
    bfclarke committed Sep 17, 2024
    Configuration menu
    Copy the full SHA
    01929c2 View commit details
    Browse the repository at this point in the history

  2. modifications for running on compute cluster

    @bfclarke
    bfclarke committed Sep 17, 2024
    Configuration menu
    Copy the full SHA
    fdcdc45 View commit details
    Browse the repository at this point in the history

  3. pipeline fix

    @bfclarke
    bfclarke committed Sep 17, 2024
    Configuration menu
    Copy the full SHA
    eb996e5 View commit details
    Browse the repository at this point in the history

  4. fix typo

    @bfclarke
    bfclarke committed Sep 17, 2024
    Configuration menu
    Copy the full SHA
    bed51b6 View commit details
    Browse the repository at this point in the history

  5. delete unused files

    @bfclarke
    bfclarke committed Sep 17, 2024
    Configuration menu
    Copy the full SHA
    6d3275e View commit details
    Browse the repository at this point in the history

  6. fixup! Format Python code with psf/black pull_request

    PMBio authored and PMBio committed Sep 17, 2024
    Configuration menu
    Copy the full SHA
    242c6b8 View commit details
    Browse the repository at this point in the history

Commits on Sep 20, 2024

  1. pipeline fixes

    @bfclarke
    bfclarke committed Sep 20, 2024
    Configuration menu
    Copy the full SHA
    3483fc6 View commit details
    Browse the repository at this point in the history

  2. pipeline fixes

    @bfclarke
    bfclarke committed Sep 20, 2024
    Configuration menu
    Copy the full SHA
    b86080a View commit details
    Browse the repository at this point in the history

  3. Merge branch 'feature/chunked-writer-precomputed-burdens-testing-comb… 

    …o' of github.com:PMBio/deeprvat into feature/chunked-writer-precomputed-burdens-testing-combo
    @bfclarke
    bfclarke committed Sep 20, 2024
    Configuration menu
    Copy the full SHA
    2662477 View commit details
    Browse the repository at this point in the history

Commits on Sep 24, 2024

  1. code cleanup

    @bfclarke
    bfclarke committed Sep 24, 2024
    Configuration menu
    Copy the full SHA
    c09eec3 View commit details
    Browse the repository at this point in the history

  2. remove unneded teest files

    @bfclarke
    bfclarke committed Sep 24, 2024
    Configuration menu
    Copy the full SHA
    0f3e2d8 View commit details
    Browse the repository at this point in the history

  3. fixup! Format Python code with psf/black pull_request

    PMBio authored and PMBio committed Sep 24, 2024
    Configuration menu
    Copy the full SHA
    c238e75 View commit details
    Browse the repository at this point in the history

  4. correct typo

    @bfclarke
    bfclarke committed Sep 24, 2024
    Configuration menu
    Copy the full SHA
    a052bd6 View commit details
    Browse the repository at this point in the history

  5. black

    @bfclarke
    bfclarke committed Sep 24, 2024
    Configuration menu
    Copy the full SHA
    7c2e867 View commit details
    Browse the repository at this point in the history

  6. Merge branch 'feature/chunked-writer-precomputed-burdens-testing-comb… 

    …o' of github.com:PMBio/deeprvat into feature/chunked-writer-precomputed-burdens-testing-combo
    @bfclarke
    bfclarke committed Sep 24, 2024
    Configuration menu
    Copy the full SHA
    14f783f View commit details
    Browse the repository at this point in the history

  7. fixup! Format Python code with psf/black pull_request

    PMBio authored and PMBio committed Sep 24, 2024
    Configuration menu
    Copy the full SHA
    1b3dfb1 View commit details
    Browse the repository at this point in the history