open2c/pairtools: v1.0.0

Major release of pairtools since April 2019 with multiple updates in the structure of code and new tools added.

• sphinx docs update with incorporated walkthroughs

• parse2 module with CLI for parsing complex walks
• scaling and header modules with CLI

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

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

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