Added `pysam` to `setup.py` `install_requires` list. Removed `cffi`. Fixed tests that were failing under Linux (apart from pyfaidx tests which are now skipped on Linux). Removed mocking `File` class and replaced it with `StringIO`. >>>>>>> master
3.0.65
Not secure
Fixed `AAread.ORFs` function in the `AARead` class and moved the `--allowOpenORFs` (True/False) check to within the function. Added a `DNAKozakRead` class. Changed `extract-ORFs.py` so that information about Kozak consensus sequences can be returned.
3.0.64
Not secure
Removed bone-headed use of full path to `fasta-join.sh` from `bin/fasta-diff.sh`.
3.0.63
Not secure
Added `compareAaReads` and `matchToString` to `aa.py`. Wrote tests in `test_aa.py` for both. Moved `countPrint` to utils, used by `matchToString` in `dna.py` and `aa.py`. Added `compare-aa-sequences.py` to the bin.
3.0.62
Not secure
Added `matchToString` to `dna.py` to allow printing of a DNA match.
3.0.61
Not secure
Added `--reverse` and `--reverseComplement` options to `filter-fasta.py` and the underlying `ReadFilter` class.