Feature/dm 191 refactor load processed pileup#21

Merged

thekugelmeister merged 29 commits intomainfrom

feature/DM-191-refactor-load-processed

May 31, 2025

Commits on Jan 8, 2025

DM-229 Consolidating parsing logic for load_processed functions. Still need to apply to export functions, and need to check that performance is unimpacted.
Oberon Dixon-Luinenburg
committed
DM-231 Removed regions=None case for pileup_counts_from_bedmethyl because it will complicate parallelization and is not clearly useful.
Oberon Dixon-Luinenburg
committed
DM-229 Adjusted export.pileup_to_bigwig to use new load_processed.process_pileup_row and renamed/configured a few variables to support this.
Oberon Dixon-Luinenburg
committed

Commits on Jan 9, 2025

Commits on Jan 10, 2025

DM-192,DM-236 Properly close and delink shared memory when appropriate to avoid intermittent crashes. Adjust tabix fetch to avoid negative start values. Tweak wording on progress bars.
Oberon Dixon-Luinenburg
committed
DM-191 Re-arrange contents of load_processed for better clarity. Added some comments.
Oberon Dixon-Luinenburg
committed

Commits on Jan 17, 2025

Commits on Jan 18, 2025

DM-239 Adjusted generate_targets module to properly handle cores argument for extract. Updated test_matrix.pickle by re-running generate_targets. No changes to pileup or extract files, but should p…

Oberon Dixon-Luinenburg
authored and
Oberon Dixon-Luinenburg
committed
Ruff format fixes

Oberon Dixon-Luinenburg
authored and
Oberon Dixon-Luinenburg
committed

Commits on Jan 27, 2025

Merge pull request #18 from streetslab/feature/DM-191-refactor-load-processed-tests-baseline
OberonDixon
authored

Commits on Feb 21, 2025

Merge branch 'main' into feature/DM-191-refactor-load-processed
OberonDixon
authored
Fixed small mistakes from merge

Oberon Dixon-Luinenburg
authored and
Oberon Dixon-Luinenburg
committed

Commits on Mar 13, 2025

Merge branch 'main' into feature/DM-191-refactor-load-processed
OberonDixon
authored

Commits on Mar 18, 2025

Added check for chrom in tabixfile.
Oberon Dixon-Luinenburg
committed

Commits on Mar 23, 2025

DM-191 Adjustments in response to PR comments from thekugelmeister
Oberon Dixon-Luinenburg
committed
Merge branch 'feature/DM-191-refactor-load-processed' of https://github.com/streetslab/dimelo_v2 into feature/DM-191-refactor-load-processed
Oberon Dixon-Luinenburg
committed

Commits on May 30, 2025

Adjust naming for regions_to_list region-splitting parallelization parameter.

Oberon Dixon-Luinenburg
authored and
Oberon Dixon-Luinenburg
committed

Commits on May 31, 2025