hic-viz

hic-viz is a simple tool that creates a contact plot from a bam file.

Compiling

hic-viz requires the graphics library GD. Currently test using GD v2.3.0

git submodule update --init --recursive

pushd src/htslib/
autoheader && autoconf
./configure
make lib-static
popd

make

Usage

Usage: hic-viz [OPTION...] <BAM>
hic-viz -- Simple hi-c contact plotting

  -o, --out FILE         Output file (default: stdout)
  -t, --type TYPE        Image format [png,jpeg,tiff,bmp] (default: png)
  -r, --region FILE      List of sequences to include (default: all)
                         Can be space, tab, or newline delimited
  -s, --plot-size INT    Size of contact map in pixels (default: 3000)
                         Actual plot will be larger due to sequence names
  -p, --palette PALETTE  Palette of contact map (default: rocket)
                         Valid options are magma, inferno, mako, rocket, or grey
  -h, --help             Give this help list
Report bugs to github.com/IGBB/hic-viz.