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`.
4.0.51
Added `--reverse` and `--complement` options to `bin/fasta-find.py` to tell it to also look for simple inversions and complement sequences.
4.0.50
Added `bin/fasta-find.py` which, like `bin/fasta-match-offsets.py`, also reports matching sequence offsets in FASTA files but can match numeric regions and also look for reverse complemented matches.