Issues

• CLI implementation of API cooler.create.append

  open2c/cooler#487 · Filter by author treznicek opened on Sep 1, 2026

• HDF5 file locking error (BlockingIOError: Resource temporarily unavailable) when cooler zoomify --balance -p > 1

  open2c/cooler#486 · Filter by author W-xyue opened on Aug 20, 2026
  1

• Add support for hdf5plugin and import it by default (maybe optionally)

  open2c/cooler#485 · Filter by author mimakaev opened on Jul 24, 2026

• specification data types

  open2c/cooler#480 · Filter by author kloetzl opened on Jan 22, 2026

• balanced contact value missing in output of cooler dump

  open2c/cooler#476 · Filter by author liu-zhiyang opened on Nov 3, 2025
  4

• whether cooler balance accounts for factors such as sequencing depth

  open2c/cooler#475 · Filter by author oganesson76 opened on Sep 9, 2025

• Hi-store

  open2c/cooler#469 · Filter by author amirbabaeyan opened on Jul 19, 2025

• cooler balance with variable size bins doesn't support --min-dist

  open2c/cooler#464 · Filter by author Phlya opened on May 1, 2025

• Compute standard deviation for expected counts/balanced.avg

  open2c/cooler#463 · Filter by author MarcoDiS opened on Apr 3, 2025

• About cooler balance

  open2c/cooler#460 · Filter by author GlenZhang-GZ opened on Mar 5, 2025

• Fix Test Failures, Improve Warning Handling, and Update Code for Stability

  open2c/cooler#459 · Filter by author ShigrafS opened on Mar 1, 2025

• Unclear Cooler.pixels().fetch behavior

  open2c/cooler#455 · Filter by author StefanoCretti opened on Jan 26, 2025
  5

• Deleting bins from scool on append leaves dead space in file

  open2c/cooler#451 · Filter by author bskubi opened on Jan 8, 2025
  4

• add rescale_marginals to CLI

  open2c/cooler#448 · Filter by author BenxiaHu opened on Dec 19, 2024
  3

• cooler cload does not accept .lz4-compressed .pairs files

  documentation
  open2c/cooler#410 · Filter by author bskubi opened on Mar 27, 2024
  1

• Allow multi enzyme digest

  enhancement
  open2c/cooler#401 · Filter by author nvictus opened on Mar 8, 2024

• Biological signal missing from cool files

  open2c/cooler#385 · Filter by author NMaziak opened on Feb 2, 2024
  2

• Store marginals (cis, total) in cooler

  enhancement
  open2c/cooler#351 · Filter by author Phlya opened on Oct 16, 2023

• Can't import cooler in aws lambda because multiprocessing is not supported

  multiprocessing
  open2c/cooler#329 · Filter by author pkerpedjiev opened on Jun 9, 2023
  3

• Upper variance limit to abort balancing?

  enhancement
  open2c/cooler#318 · Filter by author Phlya opened on Mar 29, 2023

• cooler zoomify should ensure the base resolution is properly balanced

  enhancement
  open2c/cooler#314 · Filter by author robomics opened on Feb 9, 2023

• merge .cool file of individual chromosome

  question
  open2c/cooler#293 · Filter by author chenggang108 opened on Oct 17, 2022
  1

• Can't create cooler at super high resolution

  multiprocessing
  open2c/cooler#286 · Filter by author Phlya opened on Aug 24, 2022
  1

• INFO:cooler.balance:variance is nan

  open2c/cooler#262 · Filter by author aakashsur opened on Aug 27, 2021
  1

• cooler bioframe dependency

  internals
  open2c/cooler#261 · Filter by author gfudenberg opened on Aug 24, 2021