Fixed bug in bowtie2 that was introduced by adding the `--removePrimersFromBedFile` option to `run-bowtie2.py`.
3.1.86
Not secure
Fixed two failing tests due to changed DIAMOND (version 2.0.6) bitscore calculation. If you have an older DIAMOND version you may need to update it, if you plan to run the tests.
3.1.85
Not secure
Added `--removePrimersFromBedFile` option to `run-bowtie2.py`. Fixed small bug in `codon-distance.py`.
3.1.84
Not secure
Added an option to trim primers using <b>ivar trim</b> to `run-bowtie2.py`.
3.1.83
`sam-coverage.py` now prints the min and max coverage per alignment too.
3.1.82
Not secure
Added indexing to `callHaplotypesBcftools` in `bowtie2.py`.