Graph Positional Mutations in Clusters

What's new in v0.2.0

• Generate graphs from cluster tables using graph seq, in the same manner as for tables from the relate and mask steps. Multiple types of relationships can likewise be stacked with the --stack option, and the y-axis can be toggled between ratios and counts. The --arrange option controls whether one cluster is graphed per file, all clusters from one order are graphed per file, or all clusters from all orders are graphed in one file.
• In graphing, rename "fraction" to "ratio" (which is shorter, and the same length as "count") and rename the option from --yfrac to --y-count.
• Update the color palettes for graphs to be more aesthetically pleasing and more accessible for people with impaired color vision.
• Introduce the command line option --input-file (-i) to unify the separate command line options for alignment map (BAM) files (previously -b), report files (previously -r), and table files (previously -t). The aim is to eliminate confusion among these options and free up the -r and -t short options.
• Change the short versions of command line options, including sequence read (FASTQ) files (-s -> -x, -i -> -y, and -m -> -z, as well as the uppercase versions), the temporary directory (newly -t), and table/graph relationships (-c -> -r).
• Introduce a new logo for SEISMIC-RNA, as well as the source code that generates it (seismicrna/logo/logo.py).

Full Changelog: v0.1.3...v0.2.0