Pairtools

Bugfixes:
- Drop Cython-generated .c/.cpp files from the sdist

Bugfixes:
- Migrating to pyproject.toml + cibuildwheel. pairtools will now release binary wheels for Linux. --no-build-isolation is a mandatory flag now.
- Require Cython during build to avoid the "circular import" bug.
- fix API incomplete functionality for read-side detection by agalitsyna

**Full Changelog**: https://github.com/open2c/pairtools/compare/v1.1.0...v1.1.1

Major bugfixes:
- Fix a major bug in sort that previously broke the sorting order. This bug was introduced in recent versions of pairtools 230
- Fix a major bug in dedup that caused pair duplication and broken sorting order in non-Cython backends

New features:
- stats: calculate the distance of P(s) divergence between pairs of different directionalities 222
- dedup: allow column names in all backends, and allow sorting by arbitrary columns 162

New behavior and default settings:
- dedup: turn mark-dups on by default 211
- parse: change the default --walks-policy to 5unique
- parse: pair types are now always in upper case. Previously, letters in pair types were converted to lowercase if the corresponding side contained chimeric alignments.

Minor bugfixes:
- dedup: allow inputs with quotes 194
- dedup: allow empty input pairs file 201
- stats: minor bugfixes 200

Documentation:
- a new notebook with the statistics of distances between PCR duplicates 233
- clean up phase walkthrough 218
- a new chapter on building workflows with pairtools 219 226 231
- a major cleanup

Code updates:
- make pairsio.py to read (and, in the future, write) .pairs files 195
- minor refactoring of parse 223

New Contributors:
- hkariti made their first contribution in 194

- [x] `pairtools dedup`: update default chunksize to 10,000 to prevent memory overflow on datasets with high duplication rate

- [x] `pairtools select` regex update
(string substitutions failed when the column name was a substring of another)

- [x] Warnings capture in dedup: pairs lines are always split after rstrip newline

- [x] Important fixes of splitting schema

- [x] Dedup comment removed (failed when the read qualities contained "")

- [x] Remove dbist build out of wheel

- [x] pairtools scaling: fixed an issue with scaling maximum range value https://github.com/open2c/pairtools/issues/150#issue-1439106031

- [x] Fixed issue with pysam dependencies on pip and conda

- [x] pytest test engine instead of nose

- [x] Small fixes in teh docs and scaling