Pairtools

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

Post merge:

- [x] sphinx docs update with incorporated walkthroughs

New tools:
- [x] parse2 module with CLI for parsing complex walks
- [x] scaling and header modules with CLI

Fixes by modules:

pairtools dedup
- [x] 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
- [x] chunked dedup by Phlya
- [x] improvement of dedup to include reporting of the parent readID by Phlya and agalitsyna

pairtools stats/scaling
- [x] split dedup stats and regular stats
- [x] output chromosome size to the stats output https://github.com/open2c/pairtools/issues/83
- [x] pairtools stats: YAML output? https://github.com/open2c/pairtools/issues/111 and https://github.com/open2c/pairtools/issues/79
- [x] 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
- [x] parse complex walks engine and tools: https://github.com/open2c/pairtools/pull/109
- [x] stdin and stdout reporting defaults: https://github.com/open2c/pairtools/issues/48
- [x] flipping issue: https://github.com/open2c/pairtools/issues/91

pairtools phase
- [x] make work with both pip and github versions of bwa: https://github.com/open2c/pairtools/pull/114

pairtools restrict
- [x] Handle empty pairs with "!" chromosomes: https://github.com/open2c/pairtools/issues/76
- [x] Problem with restriction sites header/first rfrag: https://github.com/open2c/pairtools/issues/73
- [x] Suggestions by golobor: https://github.com/open2c/pairtools/issues/16

pairtools merge
- [x] do not require sorting? https://github.com/open2c/pairtools/issues/23
- [x] headers handling: https://github.com/open2c/pairtools/issues/18

General improvements:

Headers maintenance
- [x] 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
- [x] transfer pairlib into sandbox of pairtools lib
- [x] separate cli and lib
- [x] Remove OrderedDict: https://github.com/open2c/pairtools/issues/113
- [x] Clean up deprecation warnings, e.g. https://github.com/open2c/pairtools/issues/71
- [x] Fix input errors without explanations, e.g. https://github.com/open2c/pairtools/issues/61

Specific changes:

Docs improvements
- [x] pairtools walkthrough
- [x] phasing walkthrough
- [x] parse docs update

Tests proposals
- [x] add tests for dedup Phlya : https://github.com/open2c/pairtools/issues/5
- [x] add tests for stats, and merge: https://github.com/open2c/pairtools/issues/5

Enhancements
- [x] add summaries: https://github.com/open2c/pairtools/pull/105
- [x] support of [bwa mem2]( https://github.com/bwa-mem2/bwa-mem2), which is 2-3 times faster than usual bwa mem: https://github.com/open2c/pairtools/discussions/118
- [x] I/O single utility instead of repetitive code in each module

* 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

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

* sort: enable lz4c compression of sorted chunks by default

* automatically convert mapq1 and mapq2 to int in `select`

* add the `flip` tool