Denovonear

fixed occasional sqlite3 error with concurrent denovonear runs

Shifted to a `denovonear` entry point for CLI purposes. Now can install and run one of:
- `denovonear cluster` (to test for clustering)
- `denovonear transcripts` (to identify transcripts containing de novos)
- `denovonear rates` (to calculate mutation rates per gene)

- Fixed bug when merging transcripts from one gene, which affected a few genes throughout the genome
- Cleaned up loading genes
- Shifted additional functions into package
- removed deprecated IDs option

- swapped clustering function inside package, now can be called from package.
- fixed occasional error when getting union of transcripts, when transcripts have
had their CDS coordinates corrected to make a complete transcript.
- separated cpp code into separate directory
- various fixes to allow for uploading to pypi for pip install
- fixed abs include and abs -> std::abs in cpp code for installs on macos via clang

- fixed merging transcripts when transcripts do not overlap
- use auto-based for-each loops in c++
- better random initialisation
- reduced merge-sort overhead in genes with extreme p-values
- allow for combining WeightedChoice objects (and underlying c++ classes)
- can use genomic coordinates in sites-specific rates

- fixed bug in sampling where genes with p-values < 1e-6 were skewed to be even more significant