Made `noninteractive-alignment-panel.py` option `--outputDir` to be required. Added error message for this in `graphics.py`.
3.0.23
Not secure
Changed the way reference sequence insertions are stored in a `dark.sam.PaddedSAM` instance to make it possible to tell which query sequences caused reference insertions.
3.0.22
Not secure
Made `dark/sam.py` properly deal with secondary alignments that are missing a SEQ.
3.0.21
Not secure
Added `sam-reference-read-counts.py` script.
3.0.20
Not secure
Updated ViralZone search URL in `dark/proteins.py`.
3.0.19
Not secure
Added `--sites` argument to `compare-dna-sequences.py` and corresponding `offsets` argument to the underlying function.