changes for droso

[nservant]

Hi Nicolas,

Thank you for the response.

I was able to get LOIC working by using the existing codebase in the github repository.

My organism of reference is drosophila, so I had to modify the code a bit to get it working.

I have some notes regarding the modifications, if you would like to incorporate the same into the package to make it more generalised for other users.

cghseg, a CRAN R package which is used by the run_seg function in lib_cnv_hic, is no longer present in CRAN and users need to download it from CRAN archives.

A function within the GLAD package, ChrNumeric, which converts non-numeric chr names to numeric ones only accepts human or mouse chromosome names. I had to replace the function within the GLAD namespace to make it work with drosophila.

when running cnv_ice.py, the script wanted symmetric matrices, with i and j being numeric names.
> But in the examples provided in the HiC-Pro package, https://github.com/nservant/HiC-Pro/blob/master/doc/MANUAL.md suggested that the names of the genome intervals should be in character format. So, later after running cnv_ice.py for the first time, I had to reconvert and reimport my Hi-C data.
> The importC function in annotate_hicdata.R forces symmetry on the HiTC object, it would be better if this was written to disk after importing, so that users can pass on the same symmetric matrix to cnv_ice.py.

Within the python package, iced/normalization/init.py line 74, it is assumed that the cnv bias vector provided has missing values (0). If this is not the case, then the package produces an error at X.sum() because subsequent calls are made to an empty array.
> It would be better to do a if any(rows_to_remove): at line 75 to check for such an occurrence before doing the operation.