Added `alsoYieldAlignments` option to `PaddedSAM.queries` method to have the returned generator also yield the `pysam.AlignedSegment` instance with the gap-padded query sequence. This makes it possible to retrieve padded queries from SAM/BAM and generate SAM/BAM (or FASTQ) of some subset of the queries.
3.0.27
Added `bin/filter-sam.py` script.
3.0.26
Made a change in `dark/dna.py`, to make `identicalMatchCount` only count non- ambiguous matches. Added testfunction `testMatchwithIdenticalAmbuguity`.
3.0.25
Not secure
Added TravisCI Slack notifications.
3.0.24
Not secure
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.