Pomoxis

Fixed
- `stats_from_bam`: handle cigar strings using `=` and `X` instead of `M`.
Changed
- Include mapping quality in `stats_from_bam` output.
Added
- Handling of LRA bams in which NM tag is number of matches rather than edit distance.
- Added an option (`-y`) to `assess_assembly` and `mini_align` to include supplementary alignments.
- Added an option (`-d`) to `mini_align` and `assess_assembly` to select minimap2 alignment preset.
- Added accumulation of errors over a number of chunks (`-a` option in `summary_from_stats` and `assess_assembly`) to get better stats.
- Use `-L` option for `minimap2`.
- Updated versions of minimap2, samtools, bcftools, bedtools, seqkit in Makefile to the most recent ones.

Fixed
- Reduced memory consumption of `catalogue_errors`.
- `fast_convert qa` now properly outputs a fasta file
- Fixed `long_fastx` `--others` option
- Fixed `split_fastx` fastq output
Added
- `assess_homopolymers` can use multiple threads

Changed
- Install `paftools.js` from minimap2 and `k8`

Changed
- Speed improvements to several benchmarking and analysis scripts
Fixed
- Quoted all variables in `mini_align` to handle spaces in inputs.

Changed
- `stats_from_bam` no longer throws exception when no alignments have been proceseed.
Added
- `coverage_from_bam` now has a `--one_file` option to better specify the output in the common usage.

Removed
- Python 3.5 support
Added
- Python >3.6 support