bug fix for unique_identifiers for merged proteome fasta and results

bug fix for merge-pg-results when multiple fasta files are provided without accompanying philosopher results

Filtering based on philosopher's set of cRAP contaminants

Filtering of CRAP contaminants in merge-proteome and merge-fasta

improvements to merge-pg-results:
-outputs table with gene information
-merged fastas now contain gene/transcript info
-defaults to filter out decoys/contaminants and fusions from merged results

filter for decoys/contaminants in proteogenomics merge functions

-allow for reference proteomes when merging proteomegenerator results
-fix for merging fasta files

merge proteomegenerator fasta and results across multiple samples

fix for glob pattern

fix for coverage calculator (searches recursively in fragpipe outputs)
update to fusion_merge to include breakpoint info