8/7/24 DL

Scripts and program to generate a suggested tree
structure that can be used as input to TGIF. Essentially
the same as the version on TGIF git repo, except a few
additional files are generated here for Supp Fig 2.

hicrep/
	HiCRep code used to calculate SCC

input/
	input matrix and bed files used for example

suggestTree.py
	program that takes in input matrices and based
	on their structural similarity measured by SCC,
	output a task tree. Same program in TGIF git
	repo, expect this version outputs a couple of
	additional auxillary files (distance.txt,
	dendrogram.pdf)

test.sh
	wrapper script to run example

output/
	output tree file from test.sh

distance.txt
dendrogram.pdf (SuppFig 2C)
	additional output files from test.sh

makeHeatmap.py
	script to visualize SCC and distance (1-SCC)
	from example

scc.pdf (SuppFig 2A)
dist.pdf (SuppFig 2B)
	output files from preceding script
