CHANGES.md

1.0.1 (2022-09-XX)

• Fixed issue with pysam dependencies on pip and conda

• pytest test engine instead of nose

• Small fixes in teh docs and scaling

1.0.0 (2022-08-XX)

This is a major release of pairtools since last release (April 2019!)

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 open2c#106 and open2c#59, also related to open2c#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 open2c#83
• pairtools stats: YAML output? open2c#111 and open2c#79
• pairtools scaling tool which takes into account chromosome sizes: open2c#81, open2c#56?

pairtools parse

• parse complex walks engine and tools: open2c#109
• stdin and stdout reporting defaults: open2c#48
• flipping issue: open2c#91

pairtools phase

• make work with both pip and github versions of bwa: open2c#114

pairtools restrict

• Handle empty pairs with "!" chromosomes: open2c#76
• Problem with restriction sites header/first rfrag: open2c#73
• Suggestions by @golobor: open2c#16

pairtools merge

• do not require sorting? open2c#23
• headers handling: open2c#18

General improvements:

Headers maintenance

• allow adding a header to a headerless file open2c#119 or broader addition of the headed module, draft: open2c#121

Code maintenance

• transfer pairlib into sandbox of pairtools lib
• separate cli and lib
• Remove OrderedDict: open2c#113
• Clean up deprecation warnings, e.g. open2c#71
• Fix input errors without explanations, e.g. open2c#61

Specific changes:

Docs improvements

• pairtools walkthrough
• phasing walkthrough
• parse docs update

Tests proposals

• add tests for dedup @Phlya : open2c#5
• add tests for stats, and merge: open2c#5

Enhancements

• add summaries: open2c#105
• support of bwa mem2, which is 2-3 times faster than usual bwa mem: open2c#118
• I/O single utility instead of repetitive code in each module

0.3.1 (2021-02-XX)

• sample: a new tool to select a random subset of pairs
• parse: add --readid-transform to edit readID
• parse: add experimental --walk-policy all (note: it will be moved to a separate tool in future!)
• all tools: use bgzip if pbgzip not available

Internal changes:

• parse: move most code to a separate _parse module
• _headerops: add extract_chromosomes(header)
• all tools: drop py3.5 support
• switch from travis CI to github actions

0.3.0 (2019-04-23)

• parse: tag pairs with missing FASTQ/SAM on one side as corrupt, pair type "XX"

0.2.2 (2019-01-07)

• sort: enable lz4c compression of sorted chunks by default

0.2.1 (2018-12-21)

• automatically convert mapq1 and mapq2 to int in select

0.2.0 (2018-09-03)

• add the flip tool

0.1.1 (2018-07-19)

• Bugfix: include _dedup.pyx in the Python package

0.1.0 (2018-07-19)

• First release.