hicAverageRegions feature request

[GinaRe]

Here is my suggestion to improve this tool:

hicPlotAverageContacts

This tool calculates and plots the average Hi-C contacts around a reference-point or scaled-regions.
Typically, the regions are TAD boundaries or scaled TADs, but any other regions defined in a BED file can be used.

hicPlotAverageContacts reference-point -m matrix.h5 --out TAD_boundaries.png
-bed TAD_boundaries.bed --referencePoint start/center/end --upstream 10000 --downstream 10000
--referenceLabel 'TAD boundaries'

hicPlotAverageContacts scale-regions -m matrix.h5 --out scaled_TADs.png
-bed TAD_domains.bed --regionBodyLength 10000 --upstream 1000 --downstream 1000
--startLabel 'TAD start' --endLabel 'TAD end'