v1.1.0

What's new in v1.1.0

Major bugfixes:

• Fix a major bug in sort that previously broke the sorting order. This bug was introduced in recent versions of pairtools #230
• Fix a major bug in dedup that caused pair duplication and broken sorting order in non-Cython backends

New features:

• stats: calculate the distance of P(s) divergence between pairs of different directionalities #222
• dedup: allow column names in all backends, and allow sorting by arbitrary columns #162

New behavior and default settings:

• dedup: turn mark-dups on by default #211
• parse: change the default --walks-policy to 5unique
• parse: pair types are now always in upper case. Previously, letters in pair types were converted to lowercase if the corresponding side contained chimeric alignments.

Minor bugfixes:

• dedup: allow inputs with quotes #194
• dedup: allow empty input pairs file #201
• stats: minor bugfixes #200

Documentation:

• a new notebook with the statistics of distances between PCR duplicates #233
• clean up phase walkthrough #218
• a new chapter on building workflows with pairtools #219 #226 #231
• major cleanup

Code updates:

• make pairsio.py to read (and, in the future, write) .pairs files #195
• minor refactoring of parse #223

New Contributors

• @hkariti made their first contribution in #194

Full Changelog: v1.0.3...v1.1.0