sanger-tol / PretextGraph

Embeds bedgraph data into Pretext contact maps.

PretextGraph

Converts bedgraph formatted data and embeds inside a Pretext contact map.

Bioconda

All commandline Pretext tools for Unix (Linux and Mac) are available on bioconda.

The full suite of Pretext tools can be installed with

> conda install pretext-suite

Or, just PretextGraph can be installed with

> conda install pretextgraph

Usage

PretextGraph reads bedgraph formatted data from stdin, e.g:

> zcat bedgraph.file.gz | PretextGraph -i input.pretext -n "graph name"
> bigWigToBedGraph bigwig.file /dev/stdout | PretextGraph -i input.pretext -n "graph name"

Important: only non-negative integer data is supported.

Options

-i input Pretext file, required. Sequence names in the Pretext file must match sequence names in the bedgraph data; although relative sort order is unimportant.
-n graph name, required. A name for the graph.

-o output Pretext file, optional. If no output is specified the graph data will be appended to the input file.

Requirments, running

4 cpu cores
128M RAM

Viewing graphs

PretextView version 0.1.2 or later.

Third-Party acknowledgements

PretextGraph uses the following third-party libraries:

• libdeflate
  
• stb_sprintf.h

Installation

Requires:

• clang >= 11.0.0
• meson >= 0.57.1

git submodule update --init --recursive
env CXX=clang meson setup --buildtype=release --unity on --prefix=<installation prefix> builddir
cd builddir
meson compile
meson test
meson install