* Fixed issue causing `bowtie2` to fail in `--fast-local` mode.
* Fixed issue causing `--soft-clipped-unmapped-tlen` to be a positional argument.
* New option `--trim-to N` causes `bowtie2` to trim reads longer
than `N` bases to exactly `N` bases. Can trim from either 3'
or 5' end, e.g. `--trim-to 5:30` trims reads to 30 bases,
truncating at the 5' end.
* Updated "Building from source" manual section with additional
instructions on installing TBB.
* Several other updates to manual, including new mentions of
[Bioconda](http://bioconda.github.io) and
[Biocontainers](https://biocontainers.pro).
* Fixed an issue preventing `bowtie2` from processing more than
one pattern source when running single threaded.
* Fixed an issue causing `bowtie2` and `bowtie2-inspect` to crash if
the index contains a gap-only segment.
* Added experimental BAM input mode `-b`. Works only with unpaired
input reads and BAM files that are sorted by read name (`samtools
sort -n`). BAM input mode also supports the following options:
o `--preserve-sam-tags`: Preserve any optional fields present in BAM record
o `--align-paired-reads`: Paired-end mode for BAM files
* Added experimental cmake support
