README

============================
=== BEDTools Version 1.2 ===
============================

Created by Aaron Quinlan Spring 2009.
Copyright 2009 Aaron Quinlan. All rights reserved.
http://people.virginia.edu/~arq5x/bedtools.html

Free for non-profit or academic use.

===Summary===  
BEDTools, prosaic as it may be, is a collection of utilities for comparing and 
intersecting genomic features in the UCSC Genome Browser BED format. 

===Installation===
1.  If you are reading this, you successfully downloaded and unzipped/unpacked the source tarball.  Great.
2.  Type "make all" at the command line.
3.  If you encountered no errors, then all of the BED Tools should now be in bin/
	If not, try to troubleshoot then email me: aaronquinlan@gmail.com
4.  Copy the files in bin/ to ~/bin or if you have the privileges, to /usr/local/bin.
5.  Use the tools.


===Acknowledgments=== 
1.  Jim Kent, UCSC.  
Much of the code herein is taken from Jim Kent's BED processing code.  
I am grateful for his elegant genome binning algorithm and therefore use it extensively.

2.  Michael Stromberg, Boston College.
I learned much of what I know about C++ style from Michael Stromberg.  I was formerly a C and Perl 
programmer and struggled to switch to C++.  The structure of BEDTools and much of the coding style
emulates Michael's. Quite honestly, this package would never exist were it not for looking through Michael's
code base. Thanks Mike!

3.  Galaxy.  
I had been using Galaxy for months prior to writing these tools.  Much of the functionality is based on what is
available on the Galaxy website.  I merely found it too slow to do several iterations of queries on a website,
especially with large sequencing datasets.  Regardless, I am grateful to the Galaxy team for creating such a
useful site that is rapidly approaching ubiquity.

4.  Ira Hall, UVa.
Discussions between Ira and I are largely the motivation for these tools.  We are frequently tracking 
down impromptu ideas and these tools were originally designed to facilitate such tangents.

5.  Royden Clark, UVa
Royden is the resident UCSC browser expert.  He has helped me immensely by teaching me how to squeeze every last bit of functionality from the 
browser.  Also, the algorithmic concept behind the genomeCoverageBed program is Royden's.

6.  Fitz Elliot, UVa
Fitz kindly taught me the ways of version control with git.  For those of who that are constantly confused by CVS and SVN, try git. I think you'll be happy.  

7. Loyal Goff, CSAIL, Broad.
Many thanks to Loyal for his assistance in making BED Tools "compilable" on the SUSE platform.  I appreciate your help and patience.


===Requests===
I would be grateful to learn of any problems or suggestions you have for improving these tools.