Francois Serra

make it use the bam file directly (but keeping the option to input matrix).

evaluate the need to do this with a separate tool, but tadbit tools would need to integrate: - comparison of compartements (plot + list of differences in bed format) -...

Bin filtering: replace cis-ratio by short-range/mid-range ratio

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plot distribution of interaction in ranges of: 20-40kb divided by 20-100kb. In this way chromosome size should not be source of bias. 

currently file type (fastq or map file) is assessed using the file name.

@david-castillo found start and end of chromsomes may be wrong. add a flag to write matrix inside JSON file

in this case tad_height should be computed on RAW data