Use `[0-9]' instead of `\d` in `bin/download-refseq-viral-gbff.sh` so that `egrep` works with the brew-installed GNU egrep on OS X.
4.0.56
Make `utils.py` `asHandle` work when passed a `pathlib.Path` argument.
4.0.55
Added `--includeAmbiguousMatches` and `--includeNonGapMismatches` options to `bin/compare-sequences.py`.
4.0.54
Added `includeAmbiguousMatches` and `includeNonGapMismatches` options to `matchToString` in `dark/dna.py`.
4.0.53
Replace use of `features` in `sam-coverage-depth.py` with the SAM file reference length, to avoid trying to use an undefined `features` variable when no reference is given.
4.0.52
Added `--force` option to `bcftools index` command in `dark/bowtie2.py`.