X-Git-Url: https://git.donarmstrong.com/?p=bamtools.git;a=blobdiff_plain;f=README;h=498f4be06dc0ecc00162c43cdaa65841cea5dff8;hp=7de7fd1d2484a4242e567da85a758a90ed0d3cb1;hb=HEAD;hpb=d37b45d132eb330a2c918c59e9ecb78168a4ac47

diff --git a/README b/README
index 7de7fd1..498f4be 100644
--- a/README
+++ b/README
@@ -1,104 +1,60 @@
-------------------------------------------------------------
+--------------------------------------------------------------------------------
 README : BAMTOOLS
-------------------------------------------------------------
+--------------------------------------------------------------------------------
 
-BamTools: a C++ API & toolkit for reading/writing/manipulating BAM files.
+BamTools provides both a programmer's API and an end-user's toolkit for handling
+BAM files.
 
-I. Introduction
-    a. The API
-    b. The Toolkit
+I.   Learn More
 
-II. Usage
-    a. The API
-    b. The Toolkit
+II.  License
 
-III. Contact
+III. Acknowledgements
 
-------------------------------------------------------------
+IV.  Contact
 
-I. Introduction:
-BamTools provides both a programmer's API and an end-user's toolkit for handling 
-BAM files.  
+--------------------------------------------------------------------------------
+I. Learn More:
+--------------------------------------------------------------------------------
 
-Ia. The API
-The API consists of 2 main modules - BamReader and BamWriter. As you would expect, 
-BamReader provides read-access to BAM files, while BamWriter does the writing of BAM
-files. BamReader provides an interface for random-access (jumping) in a BAM file,
-as well as generating BAM index files.
- 
-BamMultiReader is an extra module that allows you to manage multiple open BAM file
-for reading. It provides some validation & bookkeeping under the hood to keep all 
-files sync'ed for 
+Installation steps, tutorial, API documentation, etc. are all now available 
+through the BamTools project wiki:
 
-An additional file, BamAux.h, is included as well.  
-This file contains the common data structures and typedefs used throught the API.
+https://github.com/pezmaster31/bamtools/wiki
 
-BGZF.h & BGZF.cpp contain our implementation of the Broad Institute's 
-BGZF compression format.
+Join the mailing list(s) to stay informed of updates or get involved with 
+contributing:
 
+https://github.com/pezmaster31/bamtools/wiki/Mailing-lists
 
-Ib. The Toolkit
-If you've been using BamTools since the early days, you'll notice that our 'toy' API 
-examples (BamConversion, BamDump, and BamTrim) are now gone.  In their place is a set 
-of features we hope you find useful.
+--------------------------------------------------------------------------------
+II. License :
+--------------------------------------------------------------------------------
 
-** More explanation here **
+Both the BamTools API and toolkit are released under the MIT License.
+Copyright (c) 2009-2010 Derek Barnett, Erik Garrison, Gabor Marth,
+    Michael Stromberg
 
-usage: bamtools [--help] COMMAND [ARGS]
+See included file LICENSE for details.
 
-Available bamtools commands:
-	coverage	Prints coverage statistics from the input BAM file	
-	dump		Dump BAM file contents to text output
-	header		Prints BAM header information
-	index		Generates index for BAM file
-	merge		Merge multiple BAM files into single file
-	sort		Sorts the BAM file according to some criteria
-	stats		Prints some basic statistics from the input BAM file
+--------------------------------------------------------------------------------
+III. Acknowledgements :
+--------------------------------------------------------------------------------
 
-See 'bamtools help COMMAND' for more information on a specific command.
+ * Aaron Quinlan for several key feature ideas and bug fix contributions
+ * Baptiste Lepilleur for the public-domain JSON parser (JsonCPP)
+ * Heng Li, author of SAMtools - the original C-language BAM API/toolkit.
 
-** Follow-up explanation here **
+--------------------------------------------------------------------------------
+IV. Contact :
+--------------------------------------------------------------------------------
 
-------------------------------------------------------------
-
-II. Usage : 
-
-** General usage information - perhaps explain common terms, point to SAM/BAM spec, etc **
-
-
-IIa. The API
-
-To use this API, you simply need to do 3 things:
-
-    1 - Drop the BamTools files somewhere the compiler can find them.
-        (i.e. in your source tree, or somewhere else in your include path)
-
-    2 - Import BamTools API with the following lines of code
-        #include "BamReader.h"     // as needed
-        #include "BamWriter.h"     // as needed
-        using namespace BamTools;
-    	
-    3 - Compile with '-lz' ('l' as in Lima) to access ZLIB compression library
-	    (For VS users, I can provide you zlib headers - just contact me).
-
-See any included programs and Makefile for more specific compiling/usage examples.
-See comments in the header files for more detailed API documentation. 
-
-
-IIb. The Toolkit
-
-** More indepth overview for the toolkit commands **
-
-------------------------------------------------------------
-
-III. Contact :
-
-Feel free to contact me with any questions, comments, suggestions, bug reports, etc.
-  - Derek Barnett
+Feel free to contact me with any questions, comments, suggestions, bug reports,
+    etc.
 
+Derek Barnett
 Marth Lab
 Biology Dept., Boston College
 
-Email: barnetde@bc.edu  
-Project Websites: http://github.com/pezmaster31/bamtools   (ACTIVE SUPPORT)
-                  http://sourceforge.net/projects/bamtools (major updates only)
+Email: derekwbarnett@gmail.com
+Project Website: http://github.com/pezmaster31/bamtools