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

• do not require sorting? #23
• headers handling: #18

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

• add tests for dedup @Phlya : #5
• add tests for stats, and merge: #5

Enhancements

• add summaries: #105
• support of bwa mem2, which is 2-3 times faster than usual bwa mem: #118
• I/O single utility instead of repetitive code in each module