Hicstuff

* The docker image is now based on the miniconda3 layer, which greatly reduces build times.
* P(s) normalization factor is only computed based on P(s) values within xlim. Before that, all values above the lower bound were used. Because longer distances have much lower interaction values, this makes a small difference in practice.

New `--min` option in hicstuff view to set minimum colorscale value. Modify `--max` option to support raw values.

When indexing is required, hicstuff pipeline now generates the index in the run's temporary folder to avoid conflict between concurrent hicstuff pipeline instances. Index detection is more robust and edge cases are better handled.

* Make iteralign output name-sorted alignments
* Make replace all temporary SAM files from iteralign by BAM files
* Remove extraneous sorting step when using iteralign

* PCR filter now works as expected (removes all fragments with both reads at exact same coordinates except 1)
* scalogram now accepts genomic coordinates for range and index options

* Fixed a bug that crashed `hicstuff view` when computing a matrix ratio without using -n and -l.
* Fixed a bug in `hicstuff pipeline` that caused some pairs not to be flipped correctly
* Added support for pairs files as input in `hicstuff distancelaw`