updating ssm functions to read from latest deblacklsited maf

[mattssca]

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[mattssca]

The follwoing functions have been updated to load data from the latest (and greatest) deblacklsited mafs and to filter out varaints with low read support:

get_ssm_by_sample get_coding_ssm get_ssm_by_region get_ssm_by_gene (function removed and added "these_genes" parameter to get_ssm_by_sample and get_ssm_by_samples to allow for gene-subsetting). get_coding_ssm_status assign_cn_to_ssm (using updated get_ssm_by_samples)

The updated functions have been tested and also testing other functions that call these functions. See lsited functions bellow for such cases.

get_ssm_by_regions calc_mutation_frequency_sliding_windows get_ashm_count_matrix ashm_multi_rainbow_plot - broken due to get gamblr meta ashm_rainbow_plot annotate_driver_ssm estimate_purity fancy_sv_chrdistplot fancy_snp_chrdistplot fancy_svbar fancy_cnlohbar fancy_vplot

Package documentation has also been regenerated

[mattssca]

Thanks for your comments Ryan, here are the two items that needs to be addressed, potentially in another PR?

1. Have get_coding_ssm_status call get_coding_ssm directly to reduce duplicated code.
2. annotate_driver_ssm still calls get_ssm_by_gene. This needs to be updated.