.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.15.
.TH COOLER "1" "June 2020" "cooler 0.8.7" "User Commands"
.SH NAME
cooler \- sparse, compressed, binary persistent storage
.SH SYNOPSIS
.B cooler
[\fI\,OPTIONS\/\fR] \fI\,COMMAND \/\fR[\fI\,ARGS\/\fR]...
.SH 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.
.P
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.
.SH OPTIONS
.TP
\fB\-v\fR, \fB\-\-verbose\fR
Verbose logging.
.TP
\fB\-d\fR, \fB\-\-debug\fR
On error, drop into the post\-mortem debugger shell.
.TP
\fB\-V\fR, \fB\-\-version\fR
Show the version and exit.
.TP
\fB\-h\fR, \fB\-\-help\fR
Show this message and exit.
.SS "Commands:"
.TP
cload
Create a cooler from genomic pairs and bins.
.TP
load
Create a cooler from a pre\-binned matrix.
.TP
merge
Merge multiple coolers with identical axes.
.TP
coarsen
Coarsen a cooler to a lower resolution.
.TP
zoomify
Generate a multi\-resolution cooler file by coarsening.
.TP
balance
Out\-of\-core matrix balancing.
.TP
info
Display a cooler's info and metadata.
.TP
dump
Dump a cooler's data to a text stream.
.TP
show
Display and browse a cooler in matplotlib.
.TP
makebins
Generate fixed\-width genomic bins.
.TP
digest
Generate fragment\-delimited genomic bins.
.TP
csort
Sort and index a contact list.
.TP
ls
List all coolers inside a file.
.TP
cp
Copy a cooler from one file to another or within the same file.
.TP
ln
Create a hard link to a cooler (rather than a true copy) in the...
.TP
mv
Rename a cooler within the same file.
.TP
tree
Display a file's data hierarchy.
.TP
attrs
Display a file's attribute hierarchy.
.SH AUTHOR
 This manpage was written by Andreas Tille for the Debian distribution and
 can be used for any other usage of the program.