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TASK-5387 - Add Polygenic Scores (PGS) - #697

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jtarraga wants to merge 187 commits into

developfrom

TASK-5387

Open

TASK-5387 - Add Polygenic Scores (PGS)#697
jtarraga wants to merge 187 commits into
developfrom
TASK-5387

Commits on Dec 18, 2023
- lib: download polygenic scores (PGS), #TASK-5406, #TASK-5387
  jtarraga
  committed
  278fdbd
Commits on Dec 19, 2023
Commits on Dec 22, 2023
Commits on Jan 2, 2024
- lib: add support for annotating using PGS, #TASK-5411, #TASK-5387
  jtarraga
  committed
  314786d
Commits on Jan 3, 2024
- lib: add PGS data for variant annotation, #TASK-5411, #TASK-5387
  jtarraga
  committed
  b0aeca4
- lib: add MongoDB indexes for PGS collections, #TASK-5410, #TASK-5387
  jtarraga
  committed
  c6c628b
Commits on Jan 21, 2024
- download: gwas catalog fixes
  imedina
  committed
  6346c97
Commits on Jan 29, 2024
- lib: take into account the NumberFormatException, #TASK-5407, #TASK-5387
  jtarraga
  committed
  d343315
Commits on Feb 2, 2024
- lib: improve PGS builder, #TASK-5407, #TASK-5387
  jtarraga
  committed
  268f591
- lib: remove System.out in PGS builder, #TASK-5407, #TASK-5387
  jtarraga
  committed
  5972c15
Commits on Feb 7, 2024
- lib: filter contigs (only chromosomes) when processing PGS scores, #TASK-5407, #TASK-5387
  jtarraga
  committed
  d9ad898
- lib: minor changes, #TASK-5407, #TASK-5387
  jtarraga
  committed
  d3ad8c9
Commits on Mar 1, 2024
- Merge branch 'TASK-5392' into TASK-5564
  imedina
  committed
  19368e6
- Update configuration.yml
  imedina
  committed
  89264c2
Commits on Mar 7, 2024
Commits on Mar 8, 2024
- lib: improve gene downloader by updating versions from config file, adding log messages, removing hardcode filenames, sonnar issues,..., #TASK-5775, #TASK-5564
  jtarraga
  committed
  4cdd046
- lib: improve repeat downloader by updating versions from config file, adding log messages, removing hardcode filenames, sonnar issues,..., #TASK-5775, #TASK-5564
  jtarraga
  committed
  3cea3f3
Commits on Mar 22, 2024
- lib: improve conservation downloader by updating versions from config file, adding log messages, removing hardcode filenames, sonnar issues,..., #TASK-5775, #TASK-5564
  jtarraga
  committed
  f308f25
Commits on Mar 28, 2024
- lib: update regulation download manager, and the configuration file, to take into account the version for miRBase and miRTarBase, #TASK-5775, #TASK-5564
  jtarraga
  committed
  2e6e895
Commits on Apr 3, 2024
- lib: update configuration file; and create version files for COSMIC and HGMD; and fix some sonnar issues, #TASK-5775, #TASK-5564
  jtarraga
  committed
  a6688d0
- lib: update CellBase builder for clinical variants, #TASK-5776, #TASK-5564
  jtarraga
  committed
  c2345d4
Commits on Apr 4, 2024
- lib: fix Gwas Catalog builder for clinical variants, #TASK-5776, #TASK-5564
  jtarraga
  committed
  df0f1e0
Commits on Apr 5, 2024
- lib: refactor code by changing the DownloadProperties.URLProperties, #TASK-5775, #TASK-5564
  jtarraga
  committed
  d4cba15
Commits on Apr 11, 2024
Commits on Apr 12, 2024
- lib: update CellBase downloaders, #TASK-5775, #TASK-5564
  jtarraga
  committed
  e18506b
Commits on Apr 15, 2024
- core: update CellBase configuration file, #TASK-5775, #TASK-5564
  jtarraga
  committed
  69a58bf
Commits on Apr 18, 2024
Commits on Apr 19, 2024
- lib: update gene downloader (specially for ensembl data), and improve log messages, #TASK-5564
  jtarraga
  committed
  55afe6b
- Merge branch 'TASK-5564' into TASK-5387
  jtarraga
  committed
  d81b68f
Commits on Apr 22, 2024
Commits on Apr 23, 2024
Commits on Apr 24, 2024
Commits on Apr 25, 2024
Commits on Apr 26, 2024
Commits on Apr 29, 2024
Commits on May 7, 2024
Commits on May 8, 2024
- core: fix PGS section in the configuration file, #TASK-5406, #TASK-5387
  jtarraga
  committed
  a25b9c1
- app: add PGS_DATA (polygenic scores) as valid data in the CellBase builder, #TASK-5407, #TASK-5387
  jtarraga
  committed
  df05c91
Commits on May 10, 2024
Commits on May 11, 2024
- lib: include SpliceAI/MMSplice in the configuration file, and create the splice score downloader to create the splice score version files, #TASK-5575, #TASK-5564
  jtarraga
  committed
  57c6f6f
- lib: remove deprecated functions, #TASK-5575, #TASK-5564
  jtarraga
  committed
  c131459
Commits on May 15, 2024
Commits on May 16, 2024
- lib: improve gene downloader by taking into account the manually downloaded files and creating the data source version files, #TASK-5575, #TASK-5564
  jtarraga
  committed
  a8a047c
Commits on May 17, 2024
- lib: update gene builder (Ensembl/RefSeq) according to last changes, #TASK-5576, #TASK-5564
  jtarraga
  committed
  100d6f3
- Merge branch 'TASK-5564' into TASK-5387
  jtarraga
  committed
  1852f3e
Commits on May 18, 2024
- lib: refactor PGS builder to solve the RocksDB issue, #TASK-5407, #TASK-5387
  jtarraga
  committed
  910ffd3
Commits on May 20, 2024
- lib: improve PGS builder by speeding-up RocksDB, #TASK-5407, #TASK-5387
  jtarraga
  committed
  3939ac3
Commits on May 27, 2024
Commits on Jun 22, 2024
- Merge branch 'develop' into TASK-5564
  imedina
  committed
  4d965d7
Commits on Jun 23, 2024
- lib: add hpo filter to GeneQuery
  imedina
  committed
  fc65d14
Commits on Jul 2, 2024
- Many improvements and fixes:
  imedina
  committed
  84ad97b
- * Add new ensembl_canonical.pl
  imedina
  committed
  aaec065
- Merge branch 'TASK-5564' of https://github.com/opencb/cellbase into TASK-5564
  jtarraga
  committed
  dad180d
- lib: use DockerUtils to execute Perl script from docker image, #TASK-5775, #TASK-5564
  jtarraga
  committed
  694b81d
Commits on Jul 3, 2024
- test: update JUnit tests, #TASK-5564
  jtarraga
  committed
  c8e719a
- cicd: update task.yml to deploy cellbase-builder docker, #TASK-5564
  jtarraga
  committed
  19efdf4
Commits on Jul 4, 2024
- build: create the MiRTarBase parser for .xlsx files, #TASK-5576, #TASK-5564
  jtarraga
  committed
  fcbb680
- Builder improvements and several data cleaning
  imedina
  committed
  10a579a
- Merge branch 'TASK-5564' of github.com:opencb/cellbase into TASK-5564
  imedina
  committed
  87d95e8
- Gene downloader fixes
  imedina
  committed
  c6bcbdd
Commits on Jul 5, 2024
- Add VariationDownloader
  imedina
  committed
  0a6a84f
- Add VariationDownloader
  imedina
  committed
  3dcad47
Commits on Jul 8, 2024
- app: update Dockerfile for cellbase-builder in order to allow the script ensembl_canonical.pl to create sub-folders, #TASK-5575, #TASK-5564
  jtarraga
  committed
  5eb33ae
- Merge branch 'TASK-5564' of https://github.com/opencb/cellbase into TASK-5564
  jtarraga
  committed
  f44dcc5
Commits on Jul 9, 2024
- lib: add variation to the EtlCommons dataVersionFilenamesMap, #TASK-5575, #TASK-5564
  jtarraga
  committed
  2b226fe
Commits on Jul 22, 2024
- Merge branch 'develop' into TASK-5564
  jtarraga
  committed
  510819c
Commits on Jul 23, 2024
Commits on Jul 24, 2024
Commits on Jul 25, 2024
Commits on Jul 26, 2024
Commits on Jul 29, 2024
- lib: fix protein builder, #TASK-5576, #TASK-5564
  jtarraga
  committed
  039aa81
- lib: fix gene downloader for RefSeq files, #TASK-5575, #TASK-5564
  jtarraga
  committed
  7f77dec
Commits on Jul 31, 2024
Commits on Aug 1, 2024
Commits on Aug 2, 2024
Commits on Aug 5, 2024
Commits on Aug 6, 2024
Commits on Aug 7, 2024
Commits on Aug 8, 2024
Commits on Aug 9, 2024
- lib: fix the function to save status and message of the downloaded files; improve summary log and update downloader managers according to these changes, #TASK-5575, #TASK-5564
  jtarraga
  committed
  1f3572c
Commits on Aug 10, 2024
- Merge branch 'develop' into TASK-5564
  jtarraga
  committed
  6056655
- core: add dbSNP in config file (removed after merging), #TASK-5564
  jtarraga
  committed
  a8d6368
Commits on Aug 13, 2024
- Merge branch 'TASK-5564' into TASK-5387
  jtarraga
  committed
  2950c0e
Commits on Sep 12, 2024
- lib: limit WriteBatch for number of items, #TASK-5407, #TASK-5387
  jtarraga
  committed
  2889192
Commits on Oct 1, 2024
- lib: improve PGS builder, #TASK-5407, #TASK-5387
  jtarraga
  committed
  8c8a4ea
- lib: fix sonnar issues, #TASK-5407, #TASK-5387
  jtarraga
  committed
  28a57ba

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