Smallgenomeutilities

- [bugfix] recent versions of BioPython have deprecated functionality
used by frameshift_deletions_checks (.position, nogap, wrappers)

- frameshift_deletions_checks: `--chain` option as alternative to running `mafft`
- packaging modernized

Bugfixes:

- frameshift_deletions_checks: fixes bugs in interactions between stop codons and indels
- aln2basecnt: avoid crashes on empty sequences (e.g.: after primer trimming with samtools)

- Multiple bug and deprecation fixes and updates in framshift reporting script
- Increased portability

What's Changed
* Save aligned consensus by mcarrara-bioinfo in https://github.com/cbg-ethz/smallgenomeutilities/pull/15
* Add stop codons detection and reporting in the frameshift_deletions_check script by mcarrara-bioinfo in https://github.com/cbg-ethz/smallgenomeutilities/pull/16

New Contributors
* mcarrara-bioinfo made their first contribution in https://github.com/cbg-ethz/smallgenomeutilities/pull/15

**Full Changelog**: https://github.com/cbg-ethz/smallgenomeutilities/compare/0.3.6...0.3.7