Muller

- Added multiprocessing support. The scripts can now use multiple processes to calculate the pairwise distances between mutations (by far the longest step, especially for large datasets). The number of processes can be configured using the `--threads` option.
- The output muller and timeseries plots now scale with dataset size.
- beta: added a `--filename-pairwise` option to allow users to provide the pairwise distance calculation results from a previous analysis. This is aimed at avoiding re-calculating large datasets which may take a while to compute.
- Switched to a pure python implementation of the `get_Muller_df` function from ggmuller and removed the dependancy on `r`. This also eliminated an issue which prevented the muller plots from being generated for large datasets.
- Added a `--highlight` and `--highlight-color` options to highlight specific series relevant to the user's interest. These options accept either a genotype name or a specific gene name and color in the corresponding series.
- Renamed the Muller.py script to lineage. This is more consistent with the purpose of the scripts.

- Added additional options to control how individual mutational trajectories are filtered:
- `--disable-filter-single`: Allows mutations detected at a single time point to pass the filters.
- `--disable-filter-startsfixed`: Allows mutations which start the experiment fixed to pass the filters
- `--filter-constant`: Sets the maximum delta a trajectory must obtain in order to pass the filters. Default is 0.10 (AKA 10%), set it to 0 to disable this filter.
- `--dissable-all-filters`: Renamed from `--no-filter`. Disables all filters.
- Modified how the graphics were generated. Each graphic is now saved as both a `.png` file and as a rendered `.svg` file. The render can be disabled using the `--no-render` flag.
- Genotypes can now be selected using extracted annotation data (ex. 'A134D') form the input dataset. This is currently implemented when manually setting the color of genotypes using the `--genotype-colors` flag, but will be extended to manually setting genotypes and lineage.] in a later update.

- Fixed a major bug when inferring the lineage of genotypes. The scoring method incorrectly incremented the score by the `derivative_cutoff` value rather than the actual calculated score.

- The scripts now attempt to convert `.csv` files that are encoded differently than expected. This mainly affected csv files generated on Macs.

- Changed some log messages.

- Increased the font size for the labels on some of the generated graphs.

- The scripts now attempt to load the first sheet by default when reading excel files rather than assuming the first sheet is named 'Sheet1'.

- Added additional trajectory filters
- Trajectories must now vary in frequency by 10% over the course of the experiment. This excludes trajectories which remain constant.
- Trajectories with a single data point are now excluded from the analysis
- Trajectories which are fixed at the initial timepoint (timepoint "0") are now removed.

- Added a `--include-single` flag to disable the filter which removes trajectories which are only detected once.

- Initial version available on pypi and install-able via pip.
- The trajectories which are rejected due to the trajectories_check method are now correctly reported in the output files.
- Updated the documentation to match pypi's intended usage.

- Added confidence intervals to the lineage diagram
- Added a table to the supplementary_files folder which reports the confidence scores between all tested pairs of nested genotypes.
- Added a progress bar for large datasets which may take a while to calculate the pairwise distances.
- The trajectories which are rejected are now reported in the output.

- Fixed a bug that disabled `--similarity-cutoff`