X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=README;h=498f4be06dc0ecc00162c43cdaa65841cea5dff8;hb=4106e787c888bb743fdd778e4f3a9d241cc895f5;hp=82c9efd02ba1f239d6ed39bd1406a35f0e94d15f;hpb=b3477d029914521bb7058941ea837a00144bd512;p=bamtools.git

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+++ b/README
@@ -1,56 +1,60 @@
-------------------------------------------------------------
+--------------------------------------------------------------------------------
 README : BAMTOOLS
-------------------------------------------------------------
+--------------------------------------------------------------------------------
 
-BamTools: a C++ API for reading/writing BAM files.
+BamTools provides both a programmer's API and an end-user's toolkit for handling
+BAM files.
 
-I.   Introduction
-II.  Usage
-III. Contact
+I.   Learn More
 
-------------------------------------------------------------
+II.  License
 
-I. Introduction:
+III. Acknowledgements
 
-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.
- 
-An additional file, BamAux.h, is included as well.  
-This file contains the common data structures and typedefs used throught the API.
+IV.  Contact
 
-BGZF.h & BGZF.cpp contain our implementation of the Broad Institute's 
-BGZF compression format.
+--------------------------------------------------------------------------------
+I. Learn More:
+--------------------------------------------------------------------------------
 
-BamConversion, BamDump, and BamTrim are 3 'toy' examples on how the API can be used.
+Installation steps, tutorial, API documentation, etc. are all now available 
+through the BamTools project wiki:
 
-------------------------------------------------------------
+https://github.com/pezmaster31/bamtools/wiki
 
-II. Usage : 
+Join the mailing list(s) to stay informed of updates or get involved with 
+contributing:
 
-To use this API, you simply need to do 3 things:
+https://github.com/pezmaster31/bamtools/wiki/Mailing-lists
 
-    1 - Drop the BamTools files somewhere the compiler can find them.
-        (i.e. in your source tree, or somewhere else in your include path)
+--------------------------------------------------------------------------------
+II. License :
+--------------------------------------------------------------------------------
 
-    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).
+Both the BamTools API and toolkit are released under the MIT License.
+Copyright (c) 2009-2010 Derek Barnett, Erik Garrison, Gabor Marth,
+    Michael Stromberg
 
-See any included programs and Makefile for more specific compiling/usage examples.
-See comments in the header files for more detailed API documentation. 
+See included file LICENSE for details.
 
-------------------------------------------------------------
+--------------------------------------------------------------------------------
+III. Acknowledgements :
+--------------------------------------------------------------------------------
 
-III. Contact :
+ * 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.
 
-Feel free to contact me with any questions, comments, suggestions, bug reports, etc.
-  - Derek Barnett
+--------------------------------------------------------------------------------
+IV. Contact :
+--------------------------------------------------------------------------------
 
-Email: barnetde@bc.edu  
-Project Website: http://sourceforge.net/projects/bamtools
+Feel free to contact me with any questions, comments, suggestions, bug reports,
+    etc.
+
+Derek Barnett
+Marth Lab
+Biology Dept., Boston College
+
+Email: derekwbarnett@gmail.com
+Project Website: http://github.com/pezmaster31/bamtools