hic2gcmap - convert hic file to gcmap

Hic files as described in [1] can be converted to gcmap.

Usage:

usage: gcMapExplorer hic2gcmap [-h] [-c A B | -l] [--compression C] [-r R]
                               [-n N] [--downsampling D]
                               input [output]

Arguments:

positional arguments:
  input                 hic input file
  output                output file or directory

optional arguments:
  -h, --help            show this help message and exit
  -c A B, --chromosomes A B
                        a pair of chromosomes A B
  -l, --list            list all available chromosomes
  --compression C       compression type, choose between lzf, gzip (default:
                        lzf)
  -r R, --resolution R  the resolution, as an integer or as kb (default:
                        finest)
  -n N, --norm N        the type of norm to use, choose between VC, VC_SQRT,
                        KR, none (default: none)
  --downsampling D      the downsampling method to use, choose between sum,
                        mean, max, none (default: sum)

Examples:

Import all chromosome pairs at the finest available resolution:

gcMapExplorer hic2gcmap input.hic

List all available chromosomes:

gcMapExplorer hic2gcmap input.hic --list

Import chromosome pair X X and save output to output.gcmap:

gcMapExplorer hic2gcmap input.hic ouput.gcmap -c X X

Same as above but save to a generated filename in outdir/ using finest resulution 10kb:

gcMapExplorer hic2gcmap input.hic outdir/ -c X X -r 10kb

References:

[1]	Durand, Neva C. et al. Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments, Cell Systems, Volume 3, Issue 1, p. 95-98.