Dropped the `FastaFaiIndex` class. Use `SqliteIndex` instead. Fixed two skipped Python 3 tests (for gzipped and bz2'd file reading).
3.1.88
Not secure
Another attempt to fix the bug in bowtie2 that was introduced by adding the `--removePrimersFromBedFile` option to `run-bowtie2.py`.
3.1.87
Not secure
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`.