Added `whitelistFile` and `blacklistFile` to `ReadsAlignmentsFilter` class in `dark/alignments.py`.
3.0.35
Not secure
Fixed small bug in `filter-hits-to-fasta.py`.
Added flushing of intermediate output in `noninteractive-alignment-panel.py`.
3.0.34
Not secure
Factored common SAM filtering code out into `dark.sam.SAMFilter`. Split common FASTA command-line options into those for filtering (this is just inclusion/exclusion) and those for editing (which change the FASTA records in some way).
3.0.33
Not secure
Added `compare-consensuses.py` script.
3.0.32
Not secure
Added `bin/newick-to-ascii.py` script.
3.0.31
Not secure
Added `storeQueryIds` option to `PaddedSAM.queries` method.