COOLER

NAME

cooler - sparse, compressed, binary persistent storage

SYNOPSIS

cooler [OPTIONS] COMMAND [ARGS]...

DESCRIPTION

Cooler is a support library for a sparse, compressed, binary persistent storage format, also called cooler, used to store genomic interaction data, such as Hi-C contact matrices.

The cooler file format is an implementation of a genomic matrix data model using HDF5 as the container format. The cooler package includes a suite of command line tools and a Python API to facilitate creating, querying and manipulating cooler files.

OPTIONS

-v, --verbose

Verbose logging.

-d, --debug

On error, drop into the post-mortem debugger shell.

-V, --version

Show the version and exit.

-h, --help

Show this message and exit.

Commands:

	cload		Create a cooler from genomic pairs and bins.
	load		Create a cooler from a pre-binned matrix.
	merge		Merge multiple coolers with identical axes.

coarsen

Coarsen a cooler to a lower resolution.

zoomify

Generate a multi-resolution cooler file by coarsening.

balance

Out-of-core matrix balancing.

	info		Display a cooler’s info and metadata.
	dump		Dump a cooler’s data to a text stream.
	show		Display and browse a cooler in matplotlib.

makebins

Generate fixed-width genomic bins.

digest

Generate fragment-delimited genomic bins.

	csort		Sort and index a contact list.
	ls		List all coolers inside a file.
	cp		Copy a cooler from one file to another or within the same file.
	ln		Create a hard link to a cooler (rather than a true copy) in the...
	mv		Rename a cooler within the same file.
	tree		Display a file’s data hierarchy.
	attrs		Display a file’s attribute hierarchy.

AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and
can be used for any other usage of the program.