Overhaul graph and cycles plotting

[jluebeck]

• Add gene track showing genes & exons
  • Allow gene track to be diabled with --hide_genes
  • Allow specification of Bushman cancer gene subset with --bushman_genes
  • Change gene fontsize with --gene_fontsize
  • Specify a subset of genes with --gene_subset_list MYC PVT1...
• Separate graph and cycle plotting input file dependencies
• Unify SV arc color scheme with AA
• Add required --ref arg
• Expose --min_mapq argument
• Add --max_coverage to cap graph coverage plotting
• Slightly recolor cycles bars for visual clarity
• Rename --plot_cycles to --only_cyclic_paths
• Rebame --lr_bam to --bam
• Cycles plotting improvement to boundary edge x-axis position
• Include save as PDF
• Default DPI to 300
• Light code refactoring