Code

v0.2.0 release#26

Code

Merged

smlmbrt merged 52 commits intomainPGScatalog/pgscatalog_utils:mainfrom devPGScatalog/pgscatalog_utils:devCopy head branch name to clipboardOct 11, 2022

+2,279-422

Commits

Commits on Sep 2, 2022

• Fist commit of the 'validate' utils

  ens-lgil

  committed
  77098be

Commits on Sep 6, 2022

• Python 3.10 compatibility changes and minor updates

  ens-lgil

  committed
  08409aa

Commits on Sep 14, 2022

• Code updates and add tests for validation

  ens-lgil

  committed
  e2fc209

• Catch ftp download errors

  ens-lgil

  committed
  99eb7b1

Commits on Sep 15, 2022

• pin polars to 0.14.9

  nebfield

  committed
  5fe9fad

• bump version for next release

  nebfield

  committed
  cd7ee78

Commits on Sep 16, 2022

• Handle PGS Catalog REST API errors and retries

  ens-lgil

  committed
  96896e3

Commits on Sep 20, 2022

• Update README.md

  smlmbrt

  authored
  50b9e9e

Commits on Sep 21, 2022

• add memory profiler to development dependencies

  nebfield

  committed
  268e96a

• add support for reading zstd compressed targets

  nebfield

  committed
  012ff6d

• remove single match mode, scan_csv not compatible with bytesIO (zstd)

  nebfield

  committed
  7975951

• compress matched scorefiles

  nebfield

  committed
  b6aa2b0

• skeleton aggreggation

  nebfield

  committed
  92bd91e

• Merge pull request #19 from ens-lgil/feature/api_error

  Show description for db8f63a
  nebfield

  authored
  db8f63a

• Merge pull request #16 from ens-lgil/feature/download_error

  Show description for 98f8de7
  nebfield

  authored
  98f8de7

Commits on Sep 22, 2022

• add aggregate_score

  nebfield

  committed
  da0105e

• Cleanup the code, ignore some user warnings from pandas_schema and updatepoetry files

  ens-lgil

  committed
  85715dc

• Attempt to fix poetry error

  ens-lgil

  committed
  60e3d9f

• Fix version discrepancies for numpy

  ens-lgil

  committed
  f6d727f

• Fix path to the 'validate' test data files

  ens-lgil

  committed
  13216fe

Commits on Sep 23, 2022

• Update the README file

  ens-lgil

  committed
  b60b0aa

Commits on Sep 27, 2022

• fix df truthiness

  nebfield

  committed
  1881c17

• fix bumped version

  nebfield

  committed
  3bf62c3

• batch process input to reduce memory usage

  nebfield

  committed
  f02c58c

• read uncompressed data with a bufferedreader

  nebfield

  committed
  ae8ce14

Commits on Sep 28, 2022

• add lazy evaluation

  nebfield

  committed
  3bb3e3d

Commits on Sep 30, 2022

• improve RAM usage

  nebfield

  committed
  a559d76

Commits on Oct 3, 2022

• fix reading bim files

  nebfield

  committed
  5c15a67

• fix tests

  nebfield

  committed
  0dc745d

• fix types

  nebfield

  committed
  ba793fb

Commits on Oct 4, 2022

• Merge pull request #22 from ens-lgil/feature/scoring_file_validator

  Show description for 7bc290c
  nebfield

  authored
  7bc290c

• Merge branch 'dev' into compress

  nebfield

  authored
  470265d

• update poetry lock file

  nebfield

  committed
  a171e5b

• treat lists of files consistently

  nebfield

  committed
  593757c

• Setup a user agent for the download_scorefiles utils (REST API calls to the PGS Catalog)

  ens-lgil

  committed
  353d8f2

• Improve library call

  ens-lgil

  committed
  cc41b4f

• don't hold scorefiles in memory when combining them

  nebfield

  committed
  4eec95b

• check if input and outputs are empty in combine_scorefiles

  nebfield

  committed
  03699e2

• Handle case where we might be removing the missing variants (not default)

  smlmbrt

  committed
  50b1517

Commits on Oct 5, 2022

• add parameter for n_threads, set POLARS_MAX_THREADS with it

  nebfield

  committed
  0a5dfbe

• move dropping multiallelics from preprocessing to labelling

  nebfield

  committed
  ca1734e

• move skipping flips from matching to labelling

  nebfield

  committed
  8f1f771

Commits on Oct 6, 2022

• is_flipped -> match_flipped, fix uppercase match type

  nebfield

  committed
  f5b64cf

Commits on Oct 7, 2022

• move label_matches from get_all_matches to match_variants

  nebfield

  committed
  5b18299

• fix setting n_threads when reading

  nebfield

  committed
  df44d9b

• fix tests

  nebfield

  committed
  be96d14

Commits on Oct 10, 2022

• add sort by match type

  nebfield

  committed
  d5cfcf0

• fix _match_multiple_targets

  nebfield

  committed
  126f153

• oops

  nebfield

  committed
  6aee170

• Merge pull request #20 from PGScatalog/compress

  Show description for 4443ea3
  nebfield

  authored
  4443ea3

• Merge pull request #25 from ens-lgil/feature/user_agent

  Show description for d3da286
  nebfield

  authored
  d3da286

Commits on Oct 11, 2022

• Update pyproject.toml

  Show description for 4a21393
  smlmbrt

  authored
  4a21393