Plotting was originally built for comparing cactus and dipcall alignments between the reference and a set of given assemblies. Edit and run plot_alignment_depth.py to make plots.
Goal of plot_alignment_depth: For each subregion "bin" of the reference, plot the average number of times that subregion is aligned to a chosen assembly. Scale for every possible asm.
Input: * liftover file, generated srcGenome [asm], srcBed [entire expanse of asm], tgtGenome [ref]. This means that the liftover bed is in terms of reference coordinates.
* dipcall file, between the same asm and ref.
* number of bins to subdivide the reference into
* total length of reference
Output: * Bar plot of average mapping depth for each subregion of the reference.