Recent Releases of pairtools
pairtools - v1.1.3
Bugfixes of parse2:
[x] Standartization of complex pair types: names R1&2 and R1-2 are now uniform in the code. This was inconistent before leading to the bugs at the positions assignment for R1&2
[x] Walk policies are now applied not only to complex walks but also to non-chimeric reads in parse2
[x] New tests for parse 2
Bugfixes of pairtools select:
[x] Empty columns at the end of the .pairs file are not truncated anymore
- Python
Published by agalitsyna about 1 year ago
pairtools - 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: https://github.com/open2c/pairtools/compare/v1.1.0...v1.1.1
- Python
Published by golobor about 1 year ago
pairtools - 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 https://github.com/open2c/pairtools/pull/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 https://github.com/open2c/pairtools/pull/222 * dedup: allow column names in all backends, and allow sorting by arbitrary columns https://github.com/open2c/pairtools/pull/162
New behavior and default settings: * dedup: turn mark-dups on by default https://github.com/open2c/pairtools/pull/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 https://github.com/open2c/pairtools/pull/194 * dedup: allow empty input pairs file https://github.com/open2c/pairtools/pull/201 * stats: minor bugfixes https://github.com/open2c/pairtools/pull/200
Documentation: * a new notebook with the statistics of distances between PCR duplicates https://github.com/open2c/pairtools/pull/233 * clean up phase walkthrough https://github.com/open2c/pairtools/pull/218 * a new chapter on building workflows with pairtools https://github.com/open2c/pairtools/pull/219 https://github.com/open2c/pairtools/pull/226 https://github.com/open2c/pairtools/pull/231 * major cleanup
Code updates: * make pairsio.py to read (and, in the future, write) .pairs files https://github.com/open2c/pairtools/pull/195 * minor refactoring of parse https://github.com/open2c/pairtools/pull/223
New Contributors
- @hkariti made their first contribution in https://github.com/open2c/pairtools/pull/194
Full Changelog: https://github.com/open2c/pairtools/compare/v1.0.3...v1.1.0
- Python
Published by golobor almost 2 years ago
pairtools - v1.0.2
Critical fix of the PyPI building scheme and multiple minor fixes of tools:
[x]
pairtools selectregex update (string substitutions failed when the column name was a substring of another)[x] Warnings capture in dedup: pairs lines are always split after rstrip newline
[x] Important fixes of splitting schema
[x] Dedup comment removed (failed when the read qualities contained "#")
[x] Remove dbist build out of wheel
[x] pairtools scaling: fixed an issue with scaling maximum range value https://github.com/open2c/pairtools/issues/150#issue-1439106031
- Python
Published by agalitsyna over 3 years ago
pairtools - 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 https://github.com/open2c/pairtools/issues/106 and https://github.com/open2c/pairtools/issues/59, also related to https://github.com/open2c/pairtools/issues/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 https://github.com/open2c/pairtools/issues/83 - pairtools stats: YAML output? https://github.com/open2c/pairtools/issues/111 and https://github.com/open2c/pairtools/issues/79 - pairtools scaling tool which takes into account chromosome sizes: https://github.com/open2c/pairtools/issues/81, https://github.com/open2c/pairtools/issues/56?
pairtools parse - parse complex walks engine and tools: https://github.com/open2c/pairtools/pull/109 - stdin and stdout reporting defaults: https://github.com/open2c/pairtools/issues/48 - flipping issue: https://github.com/open2c/pairtools/issues/91
pairtools phase - make work with both pip and github versions of bwa: https://github.com/open2c/pairtools/pull/114
pairtools restrict - Handle empty pairs with "!" chromosomes: https://github.com/open2c/pairtools/issues/76 - Problem with restriction sites header/first rfrag: https://github.com/open2c/pairtools/issues/73 - Suggestions by @golobor: https://github.com/open2c/pairtools/issues/16
pairtools merge - do not require sorting? https://github.com/open2c/pairtools/issues/23 - headers handling: https://github.com/open2c/pairtools/issues/18
General improvements:
Headers maintenance - allow adding a header to a headerless file https://github.com/open2c/pairtools/issues/119 or broader addition of the headed module, draft: https://github.com/open2c/pairtools/pull/121
Code maintenance - transfer pairlib into sandbox of pairtools lib - separate cli and lib - Remove OrderedDict: https://github.com/open2c/pairtools/issues/113 - Clean up deprecation warnings, e.g. https://github.com/open2c/pairtools/issues/71 - Fix input errors without explanations, e.g. https://github.com/open2c/pairtools/issues/61
Specific changes:
Docs improvements - pairtools walkthrough - phasing walkthrough - parse docs update
Tests proposals - add tests for dedup @Phlya : https://github.com/open2c/pairtools/issues/5 - add tests for stats, and merge: https://github.com/open2c/pairtools/issues/5
Enhancements - add summaries: https://github.com/open2c/pairtools/pull/105 - support of bwa mem2, which is 2-3 times faster than usual bwa mem: https://github.com/open2c/pairtools/discussions/118 - I/O single utility instead of repetitive code in each module
- Python
Published by agalitsyna over 3 years ago
pairtools -
- parse: tag pairs with missing FASTQ/SAM on one side as corrupt, pair type "XX"
- Python
Published by golobor almost 7 years ago
pairtools -
- automatically convert mapq1 and mapq2 to int in
select
- Python
Published by golobor about 7 years ago