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.
3.0.30
Not secure
Added `alignmentCount` attribute to `PaddedSAM` class.
3.0.29
Not secure
Renamed `alsoYieldAlignments` option of `PaddedSAM.queries` to `addAlignment` and add the alignment to the `Read` instance instead of returning a tuple.