I am looking for a software tool which will allow me to use the directionality index to call TADs as defined by Dixon et al. 2012. I found a tool called Domain caller which I believe has been created by the authors of the paper, however Rao et al. 2014 used this tool in the supplementary methods of their paper and found that when using higher resolution data it failed on some chromosomes.
Since I want to use higher resolution data I am now looking into using a function from the R package HiTC. In order to use this I would need to convert .hic files (the format produced by Juicer) to a HTClist object.
Does anyone know how to do this? or does anyone know of any other tools implementing directionality index?