Refactored `SAMFilter` to allow filtering alignments in pileups. Added `bin/sam-coverage.py`.
3.0.67
Not secure
Use `dark.utils.StringIO` everywhere as it can be used as a context manager in Python 2.
3.0.66
Not secure
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.