Releases: open2c/pairtools
v1.1.2
v1.1.1
What's new in v1.1.1
Bugfixes:
- Pairtools migrated to pyproject.toml + cibuildwheel and will now release binary wheels for Linux. --no-build-isolation became a mandatory flag.
- Cython is now required during the build stage to avoid the "circular import" bug.
- Fix the incomplete API functionality for read-side detection.
Full Changelog: v1.1.0...v1.1.1
v1.1.0
What's new in v1.1.0
Major bugfixes:
- Fix a major bug in
sortthat previously broke the sorting order. This bug was introduced in recent versions of pairtools #230 - Fix a major bug in
dedupthat 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
Full Changelog: v1.0.3...v1.1.0
Contributors
Assets 2
v1.0.3
v1.0.2
Critical fix of the PyPI building scheme and multiple minor fixes of tools:
-
pairtools selectregex update
(string substitutions failed when the column name was a substring of another) -
Warnings capture in dedup: pairs lines are always split after rstrip newline
-
Important fixes of splitting schema
-
Dedup comment removed (failed when the read qualities contained "#")
-
Remove dbist build out of wheel
-
pairtools scaling: fixed an issue with scaling maximum range value #150 (comment)
v1.0.1
-
Fixed issue with pysam dependencies on pip and conda
-
pytest test engine instead of nose
-
Small fixes in the docs and scaling
v1.0.0
Major release of pairtools since April 2019 with multiple updates in the structure of code and new tools added.
Post merge:
- sphinx docs update with incorporated walkthroughs
New tools:
- parse2 module with CLI for parsing complex walks
- scaling and header modules with CLI
Fixes by modules:
pairtools dedup
- finalize detection of optical duplicates #106 and #59, also related to #54
- chunked dedup by @Phlya
- improvement of dedup to include reporting of the parent readID by @Phlya and @agalitsyna
pairtools stats/scaling
- split dedup stats and regular stats
- output chromosome size to the stats output #83
- pairtools stats: YAML output? #111 and #79
- pairtools scaling tool which takes into account chromosome sizes: #81, #56?
pairtools parse
- parse complex walks engine and tools: #109
- stdin and stdout reporting defaults: #48
- flipping issue: #91
pairtools phase
- make work with both pip and github versions of bwa: #114
pairtools restrict
- Handle empty pairs with "!" chromosomes: #76
- Problem with restriction sites header/first rfrag: #73
- Suggestions by @golobor: #16
pairtools merge
General improvements:
Headers maintenance
- allow adding a header to a headerless file #119
or broader addition of the headed module, draft: #121
Code maintenance
- transfer pairlib into sandbox of pairtools lib
- separate cli and lib
- Remove OrderedDict: #113
- Clean up deprecation warnings, e.g. #71
- Fix input errors without explanations, e.g. #61
Specific changes:
Docs improvements
- pairtools walkthrough
- phasing walkthrough
- parse docs update
Tests proposals
Enhancements
