Pp-sketchlib

New features:
- Allow turning off random match computation (28), which is useful for querying.
- Replace threads with OpenMP (31). Much more efficient CPU parallelisation of distances.
- Add GPU/CPU hybrid sketching algorithm for read data (32).
- Add codon phased seeds `--codon-phased` (35). This replaces randomly spaced seeds.

Bug fixes:
- Update to work with HighFive v2.2.2
- Check for zero Jaccard distances (36)

New features:
- Add parallelised sparse and dense matrix operations (21, 23)
- Used spaced seeds in hash function; store sketching version in HDF5 file (22)
- Chunk up distance calculation on the GPU, so any size is supported (24)
- Calculate random match chances via Monte Carlo simulation (27)

Added CI testing:
- Add new tests for matrix functions
- Add test for distances compared to reference values

Test to be manually run:
- Compare GPU and CPU distances

Adds the following features:
- Extract Jaccard distances
- Calculate and save genome length using minimum hash
- Calculate and save base composition
- Adjust comparisons for base composition, and expected random matches
- Spaced seeds for short k-mer lengths

Bug fixes:
- Error when calculating distances on a GPU (18)

New features:
- Distance calculations on CUDA compatible GPUs.
- Use armadillo linear solver rather than dlib for regressions (on CPU).

Added some benchmarks to the readme

New features:
* Implement countmin correctly and pick sensible default parameters for sketching read datasets (11)
* More reliable and faster code for optimiser used in linear regression
* Add testing and CI

Bug fixes:
* Made CMakeLists.txt and Makefile more general (removed specific paths)

Small fixes:

* 14: Use the `mkl_rt` library to link, which works better with conda (see https://groups.google.com/forum/#!msg/kaldi-help/m3nyQke0HS0/4fj8gkSWAgAJ, https://software.intel.com/en-us/forums/intel-math-kernel-library/topic/748309, https://github.com/ContinuumIO/anaconda-issues/issues/720)
* 14: As the sequential library cannot be specified, export this as an environment variable in the `api.cpp` functions which handle their own threading.
* Correct version of gcc used to compile