Added `bin/ids.py` script to generate incrementing lists of ids.
4.0.82
Added `start` option to `dimensionalIterator`.
4.0.81
Added `asList` option to `parseRangeString` function in `utils.py`.
4.0.80
Added `--sequenceWhitelist`, `--sequenceBlacklist`, `--sequenceWhitelistFile`, `--sequenceBlacklistFile`, `--sequenceRegex`, and `--sequenceNegativeRegex` arguments to `filter-fasta.py` to match the corresponding options for sequence titles (ids).
4.0.79
Added `--sortBy coverage` option to `bin/sam-reference-read-counts.py` and moved much of its code into `dark/sam.py`.
4.0.78
Fix tiny bug in `bowtie2.py` so that BAM is not accidentally created when removing duplicates.