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.
3.0.28
Not secure
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`.