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.