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`.
3.2.3
Not secure
Added option to use `ivar` for consensus calling in `make-consensus.py`.
3.2.1
Added warning when `--removeDuplicatesUseMD5` is used without one of `--removeDuplicates` or `--removeDuplicatesById`. Added `--tmpChmod` option to `run-bowtie2.py`.
3.2.0
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`.