DOCUMENTATION
-------------

http://portal.nersc.gov/dna/RD/Adv-Seq/ALE-doc/

This code is no longer in active development. Pull requests and bugs will be addressed as needed.

Plotting
--------

The authors recommend using IGV to view the output.

http://www.broadinstitute.org/igv/

Just import the assembly, bam and ALE scores. You can convert the .ale file to a set of .wig files with ale2wiggle.py and IGV can read those directly.  Depending on your genome size you may want to convert the .wig files to the BigWig format.

LICENSE
-------

/*
 * Copyright (C) 2010,2011,2012 Scott Clark. All rights reserved.
 *
 * Developed by:
 * Scott Clark
 * Cornell University Center for Applied Mathematics
 * http://cam.cornell.edu
 * AND
 * Rob Egan
 * Department of Energy Joint Genome Institute
 * http://jgi.doe.gov
 * 
 * Permission is hereby granted, free of charge, to any person obtaining a 
 * copy of this software and associated documentation files (the "Software"), 
 * to deal with the Software without restriction, including without limitation 
 * the rights to use, copy, modify, merge, publish, distribute, sublicense, 
 * and/or sell copies of the Software, and to permit persons to whom the 
 * Software is furnished to do so, subject to the following conditions:
 *
 *   1. Redistributions of source code must retain the above copyright notice, 
 *      this list of conditions and the following disclaimers.
 *   2. Redistributions in binary form must reproduce the above copyright 
 *      notice, this list of conditions and the following disclaimers in the 
 *      documentation and/or other materials provided with the distribution.
 *   3. Neither the names of Cornell University, The Joint Genome Institute, 
 *      nor the names of its contributors may be used to endorse or promote 
 *      products derived from this Software without specific prior written 
 *      permission.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 
 * CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING 
 * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER 
 * DEALINGS WITH THE SOFTWARE.
 */

// For more information on the licence please see
// The University of Illinois/NCSA Open Source License
// http://www.opensource.org/licenses/UoI-NCSA.php

INSTALL
-------

http://portal.nersc.gov/dna/RD/Adv-Seq/ALE-doc/index.html#installation

#
# ALE comes packaged with samtools-0.1.18  Feel free to use a later version
# samtools is open source (MIT license)
# We would like to thank the creators for the extensive and very useful package
#

Requirements for plotter4.py:
	numpy 1.6.1
	mpmath 0.17
	setuptools 0.6c11
	matplotlib 1.0.1
	pymix 0.8  http://www.pymix.org/pymix/