* Fixed an issue in BAM pattern source where one thread would prematurely
close the read file pointer resulting in other threads crashing because
of "Bad file descriptor" errors.
* Fixed an issue that would cause bowtie2 to crash with `--no-1mm-upfront`
specified
* Modified bowtie2-build script to better handle of flags and positional
parameters
* Migrated all python scripts to python3.
* Added support for wildcards in input files to bowtie2 wrapper script e.g.
`bowtie2 -x index -q *.fq as opposed to bowtie2 -x index -q 1.fq,2.fq,3.fq...`
* Fixed an issue causing bowtie2 to incorrectly process read names see
[#265](https://github.com/BenLangmead/bowtie2/issues/265)
* Added support for allowing presets to be overridden by more specific
options e.g `bowtie2 -x index --local --very-fast-local --L22 -q reads.fq`
will cause bowtie2 to use a seed length of 22 instead of a seed length
of 25 that's configured for `--very-fast-local` preset.
* Modified SAM output for `-k`/`-a` so that supplementary alignments get
assigned a MAPQ of 255.
* Fixed an issue that would cause bowtie2-build to not generate
reverse index files.
* Added preliminary support for ppc64le architectures with the help of
SIMDE project see [#271](https://github.com/BenLangmead/bowtie2/issues/271) for details.
* Fixed an issue causing bowtie2 to incorrectly calculate the MAPQ
when `--mp` was specified in combination with `--ignore-quals`.
