Pymutspec

Features:

- added availability to collect non-syn mutational spectrum
- added a couple of arguments to calculate_mutspec func: scale, drop_underrepresented (this will drop mut types less than 0.9 by default)

Fixes:

- drop Times New Roman from default font for spectrum barplots
- deleted legacy log/doc files from repo
- added few tests for expected mutations collecting funcs
- fix scripts/calculate_mutspec.py : previously it failed when there was no mutations on branches, and reduced mutnum thresholds

- Fixed uncertainty coefficient (phylocoef) calculation: based on only ingroup and geometric mean of distances from root to leaves
- Added little tests for plot functions
- Added few new functions from analysis notebooks, that used to tree spectra analysis
- General test for collect_mutations.py main class

fix calculate_mutspec.py

add some spectra annotation funcs

fix `scripts/calculate_mutspec.py` and `scripts/plot_mutspec.py` for pipeline

extend interface of the script collect_mutations.py