Added `--maskNoCoverage` option to `make-consensus.py`.
3.1.56
Not secure
Added `sequenceToRegex` function to `dark/dna.py`.
3.1.55
Not secure
Added `fasta-variable-sites.py` script.
3.1.54
Not secure
Improve the printing of ambiguous sites to not show gaps in `compare-sequences.py`.
3.1.53
Not secure
Added `--showAmbiguous` to `compare-sequences.py`. Pass `--iupac-codes` to `bcftools consensus` in `make-consensus.py`. Add `--max-depth 5000` to `bcftools mpileup` call, also in `make-consensus.py`.
3.1.52
Not secure
Make `sam-coverage-depth.py` not throw an error if there is no coverage at all.