Issues

• pr.join() strandedness="same" issue version 0.1.4

  pyranges/pyranges0#404 · Filter by author michaelway opened on Mar 27, 2026
  3

• ValueError: buffer source array is read-only when writing BigWig files

  pyranges/pyranges0#403 · Filter by author dborgesr opened on Feb 26, 2026
  5

• Fails to load BED file

  pyranges/pyranges0#400 · Filter by author olegs opened on Sep 30, 2025
  4

• Error when running read_gtf() on RefSeq MANE GTF

  pyranges/pyranges0#398 · Filter by author isaacvock opened on Sep 19, 2025
  8

• Add SQLite3 backend for performance Improvement

  pyranges/pyranges0#397 · Filter by author DhanoHacks opened on Apr 16, 2025
  7

• Can only do stranded operations when both PyRanges contain strand info

  pyranges/pyranges0#388 · Filter by author fairliereese opened on Jul 18, 2024
  2

• np.bool error in gr.head()

  pyranges/pyranges0#386 · Filter by author davidhbrann opened on Jun 14, 2024

• PyRanges read_bed produces wrong number of chromosomes when cast to categorical

  pyranges/pyranges0#375 · Filter by author mtekman opened on Feb 20, 2024
  1

• Unexpected behaviour with strandedness of pyranges object

  bug
  pyranges/pyranges0#374 · Filter by author kkuret opened on Jan 31, 2024
  8

• PyRanges.intersect - "invert=True" kwarg behavior

  pyranges/pyranges0#370 · Filter by author vincentczhou opened on Dec 8, 2023
  1

• overlap default strandedness argument incorrectly documented

  pyranges/pyranges0#364 · Filter by author cmatKhan opened on Nov 6, 2023

• count_overlaps documentation says it supports nb_cpu but it is not implemented

  pyranges/pyranges0#363 · Filter by author leetaiyi opened on Nov 1, 2023
  9

• count_overlaps causes overflow errors when number of reads are large

  pyranges/pyranges0#361 · Filter by author leetaiyi opened on Oct 25, 2023
  2

• subtract does not respect strandedness default

  pyranges/pyranges0#356 · Filter by author michaelJwilson opened on Oct 11, 2023

• Future warning when trying to find intersection between non overlapping ranges

  pyranges/pyranges0#345 · Filter by author GH-MStamboulian opened on Jul 7, 2023
  9

• Code coverage badge for README.md

  enhancementgood first issue
  pyranges/pyranges0#332 · Filter by author endrebak opened on May 19, 2023

• bedtools fixed so we can test jaccard properly

  good first issue
  pyranges/pyranges0#324 · Filter by author endrebak opened on May 18, 2023

• Make example data its own package?

  enhancementgood first issue
  pyranges/pyranges0#322 · Filter by author endrebak opened on May 17, 2023
  1

• Mapping between coordinates systems

  enhancement
  pyranges/pyranges0#315 · Filter by author marco-mariotti opened on May 16, 2023
  2

  

• Add slack argument to overlap, intersect, set_intersect, set_union

  enhancement
  pyranges/pyranges0#314 · Filter by author marco-mariotti opened on May 16, 2023
  1

  

• Improve API documentation

  enhancement
  pyranges/pyranges0#312 · Filter by author marco-mariotti opened on May 16, 2023
  

• Remove CPU-flag?

  pyranges/pyranges0#306 · Filter by author endrebak opened on May 6, 2023

• Implement correct but slow gtf/gff-reader to be used as backup.

  pyranges/pyranges0#305 · Filter by author endrebak opened on May 6, 2023
  1

• Remove support for int32 chromosome starts/ends?

  pyranges/pyranges0#302 · Filter by author endrebak opened on May 2, 2023
  5

• Overlap function met error using multi-cpus

  pyranges/pyranges0#298 · Filter by author ttbond opened on Mar 17, 2023
  2