Added `titleRegex` and `negativeTitleRegex` to `ProteinGrouper` class and `--titleRegex` and `--negativeTitleRegex` arguments to `proteins-to-pathogens.py`.
3.0.69
Not secure
Added `--title` and `--preamble` args to output from `proteins-to-pathogens.py`. Fixed `ProteinGrouper` HTML NCBI protein link and added genome link. Added positive and negative filtering by regex to `TitlesAlignments` and tests. Improved NCBI link generation and tests. >>>>>>> master
3.0.68
Not secure
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.