Issues

• Tool to translate pairs to a new coordinate system

  open2c/pairtools#287 · Filter by author prototaxites opened on Oct 1, 2026
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• No Version 1.1.3 on Pypl

  open2c/pairtools#285 · Filter by author jyw-atgithub opened on Mar 20, 2026

• scaling without specified view is broken

  open2c/pairtools#282 · Filter by author Phlya opened on Feb 2, 2026

• pairtools parse2 returns <class 'NotImplementedType'> when using --add-columns seq

  open2c/pairtools#281 · Filter by author bskubi opened on Jan 23, 2026

• Phase not updating chromosomes names in the header

  open2c/pairtools#280 · Filter by author Phlya opened on Nov 3, 2025

• bug in "select" when filtering and --remove-columns at the same time

  open2c/pairtools#279 · Filter by author sergpolly opened on Oct 28, 2025

• Install Error

  open2c/pairtools#276 · Filter by author WengangXbio opened on Sep 18, 2025

• Extract pairs based on overlaps

  open2c/pairtools#275 · Filter by author jeff-godwin opened on Aug 28, 2025

• pairtools merge fails with "Argument list too long"

  open2c/pairtools#274 · Filter by author aringeri opened on Aug 14, 2025

• Warning when running with pysam 0.23.1 leading to non-zero exit code

  open2c/pairtools#270 · Filter by author prototaxites opened on May 30, 2025
  3

• chrom1, chrom2 and pair_type fields are now required in pairs file header

  open2c/pairtools#264 · Filter by author js2264 opened on Feb 19, 2025
  4

• Identical read_len1 and read_len2 reported with different real read lengths in R1&2 pairs

  open2c/pairtools#262 · Filter by author Phlya opened on Jan 14, 2025
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• pairtools:Empty of fully duplicated library, can't estimate complexity

  open2c/pairtools#254 · Filter by author Wong718 opened on Nov 4, 2024
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• Pairtools phase - issue with phasing

  open2c/pairtools#253 · Filter by author ddepierre opened on Oct 11, 2024

• convert pairtools result to dense matrix

  open2c/pairtools#252 · Filter by author BenxiaHu opened on Sep 30, 2024

• Support for lowercase SAM tags in pairtools parse2

  open2c/pairtools#245 · Filter by author LuJiansen opened on Jul 30, 2024

• Extracting contact matrices from pairs file

  open2c/pairtools#243 · Filter by author arodel21 opened on Jul 13, 2024
  2

• pairtools dedup: invalid value encountered in divide

  open2c/pairtools#242 · Filter by author gbdnorden opened on Jun 15, 2024
  1

• Scaling by pairs error

  open2c/pairtools#240 · Filter by author DekkerBastiaan opened on May 9, 2024
  1

• Updating the ReadTheDocs

  open2c/pairtools#238 · Filter by author SaimMomin12 opened on Apr 29, 2024

• raise an error/warning if chromosome names in .chrom.sizes and bwa index differ too much

  open2c/pairtools#235 · Filter by author golobor opened on Apr 10, 2024

• Wording in pairtools parse2 for --max-insert-size

  open2c/pairtools#232 · Filter by author bskubi opened on Apr 1, 2024

• Memory overconsumption/leak (?) in pairtools restrict

  open2c/pairtools#228 · Filter by author bskubi opened on Mar 27, 2024

• parse vs parse2 difference in default behavior for --flip?

  open2c/pairtools#227 · Filter by author bskubi opened on Mar 27, 2024

• All pairs are corrupt ("XX")

  open2c/pairtools#221 · Filter by author lu-r-lu opened on Mar 23, 2024
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