Hicstuff

NEW FEATURE(S):

- Add stats module to report statistics on Hi-C library processing

CHANGES:

- `zcat` no longer needed

BUG FIXES:

- avoid `removesuffix`

NEW FEATURE(S):

- Final pairs file is now sorted and gzipped with pairtools

CHANGES:

- Docker now uses `micromamba` base image

BUG FIXES:

- cases when exclude is specified
- cheking number of reads in fastq

CHANGES:

- **`--mat_fmt=cool` by default**

NEW FEATURE(S):

- by default, an **un-binned** .cool file is generated
- if the end user provides a `--binning=INT` in pipeline, a balanced .mcool file binned at multiple resolutions will be automatically generated
- specify `--zoomify=False` to only generate a single-resolution binned .cool
- balancing arguments can be specified with `--balancing_args "..."`
- `--exclude=STR` in pipeline to remove chromosomes from the final matrix

BUG FIXES:

- check that provided fastq/bam files have the same length before starting
- cutsite doc is fixed

* Add `--binning`, `--zoomify` and `--balancing` arguments to pipeline by js2264 in https://github.com/koszullab/hicstuff/pull/76
* Fixed deprecated SeqUtils.GC
* `cooler` is a strict dependency

**Full Changelog**: https://github.com/koszullab/hicstuff/compare/v3.1.6...v3.1.7

- Use local alignment for the iterative mapping mode with bowtie2
- Update deprecated sklearn pypi package requirement
- Update the docs

- Fix file extension in hicstuff rebin.
- Fix incompatibility between lines and trim in hicstuff view.
- More flexible binning suffix support.
- Update commands.py and fix pandas >= 1.5, accordingly.