Added `--sort` option to `sam-reference-read-counts.py` to sort output (i.e., matched references) by highest number of mapped reads.
4.0.0
`btop2cigar` now returns a generator that gives the individual parts of a CIGAR string. Use `''.join(btop2cigar(...))` to get the full CIGAR string. This is not backwards compatible, hence the major version number change.
Pass the `tmpChmod` argument to a call to `Bowtie2` for which it was missing.
3.2.7
Added `--maxMatchingReads` to title fitering.
3.2.6
Not secure
Added BAM file sorting to `make-consensus.py` so ivar primer trimming actually works.
3.2.5
Not secure
Added ivar primer trimming (via the `--ivarBedFile` argument) to `make-consensus.py`.
3.2.4
Not secure
Changed how `ivarFrequencyThreshold` is set and checked in `make-consensus.py`.