Pyrodigal

Added
- `pyrodigal` command line script exposing a CLI mimicking the original `prodigal` binary.
- `write_gff`, `write_genes` and `write_translations` methods to `pyrodigal.Predictions` to write the predictions results to a file in different formats.
- Implementation for masking regions of unknown nucleotides in input sequences.

Changed
- Renamed `pyrodigal.Pyrodigal` class to `pyrodigal.OrfFinder`.

Fixed
- `setup.py` build different SIMD implementations with the same set of feature flags, causing compilers to re-optimize the SIMD implementations.

Added
- Sphinx documentation with small install guide and API reference.

Fixed
- `setup.py` not detecting SSE2 and AVX2 build support because of a linker error.

Changed
- Build OSX extension without AVX2 support since runtime detection of AVX2 to avoid the `Illegal Instruction: 4` bug on older CPUs.

Fixed
- Source distribution lacking C files necessary for building `cpu_features`.

Added
- SIMD code to build an index of which connections can be skipped when scoring node connections in the dynamic programming routine ([6](https://github.com/althonos/pyrodigal/pull/6)).

Added
- `Prediction.confidence` method to compute the confidence for a prediction like reported in Prodigal's GFF output.
- `Prediction.sequence` method get the nucleotide sequence of a predicted gene ([4](https://github.com/althonos/pyrodigal/issues/4)).

Changed
- Replaced internal storage of input sequences to use a byte array instead of a bitmap.

Fixed
- Extract `Prediction.gc_cont` number directly from the start node instead of the text representation to get full accuracy.
- Prodigal bug causing nodes on the reverse strand to always receive a penalty instead of penalizing only small ORFs ([hyattpd/Prodigal88](https://github.com/hyattpd/Prodigal/pull/88)).

Fixed
- `Prediction.translate` not translating the last unknown codon properly for genes on the direct strand.