v1.0.0

[agalitsyna]

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 detecting optical duplicates #106 and optical dedup stats #59, also related to add non-additive stat summaries to dedup/stats: complexity estimation, cis/total, ... #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 add chromsizes into pairtools stats output #83
• pairtools stats: YAML output? format pairtools stats output as YAML #111 and should we store stats as YAML (or json) #79
• pairtools scaling tool which takes into account chromosome sizes: improve distance binning for FR,RR,FR,RF pairs "scalings" in stats output #81, calculate Pc(s) in stats #56?

pairtools parse

• parse complex walks engine and tools: Parse2 update (#99) #109
• stdin and stdout reporting defaults: make auto_open default to stdin/stdout when path evaluates to False #48
• flipping issue: standalone flip fails when "reduced.chrom.sizes" provided, should go lexicographical #91

pairtools phase

• make work with both pip and github versions of bwa: pairtools phase critical update #114

pairtools restrict

• Handle empty pairs with "!" chromosomes: restrict can't handle '!' chromosome #76
• Problem with restriction sites header/first rfrag: Assignment of fragment in restrict passed the first fragment. #73
• Suggestions by @golobor: add restriction tool #16

pairtools merge

• do not require sorting? in merge, add an option to concatenate pairsam files instead of merging sorted files #23
• headers handling: in merge, add an option to take a header from the first file and ignore other headers #18

General improvements:

Headers maintenance

• allow adding a header to a headerless file CLI to add header #119
  or broader addition of the headed module, draft: Header CLI #121

Code maintenance

• transfer pairlib into sandbox of pairtools lib
• separate cli and lib
• Remove OrderedDict: ImportError: cannot import name 'Mapping' from 'collections' #113
• Clean up deprecation warnings, e.g. VisibleDeprecationWarning #71
• Fix input errors without explanations, e.g. merge without arguments #61

Specific changes:

Docs improvements

• pairtools walkthrough
• phasing walkthrough
• parse docs update

Tests proposals

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

Enhancements

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

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This discussion was created from the release v1.0.0.

[sergpolly]

Congratulations !!!