X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=README;h=498f4be06dc0ecc00162c43cdaa65841cea5dff8;hb=7f8b301e2f43d4d50a79f6184f1c132c9e33d324;hp=92f88d152efd75d0fb237577f3e14758db400beb;hpb=8fae52de6c4b9df3cc754554b915a886e0263d6f;p=bamtools.git

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+++ b/README
@@ -1,36 +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.
 
-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.
- 
-An additional file, BamAux.h, is included as well.  
-This file contains the common data structures and typedefs used throught the API.
+I.   Learn More
 
-------------------------------------------------------------
+II.  License
 
-To use this API, you simply need to do 3 things:
+III. Acknowledgements
 
-    1 - Drop the BamTools files somewhere the compiler can find them.
-        (i.e. in source directory, or somewhere in include path)
+IV.  Contact
 
-    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 'lion') to access ZLIB compression library
+--------------------------------------------------------------------------------
+I. Learn More:
+--------------------------------------------------------------------------------
 
-See any included programs and Makefile for more specific compiling/usage examples.
-See documentation & comments in header files for API details. 
+Installation steps, tutorial, API documentation, etc. are all now available 
+through the BamTools project wiki:
 
-------------------------------------------------------------
+https://github.com/pezmaster31/bamtools/wiki
 
-Feel free to contact me with any questions, comments, suggestions, bug reports, etc.
-  - Derek Barnett
-  
-http://sourceforge.net/projects/bamtools
+Join the mailing list(s) to stay informed of updates or get involved with 
+contributing:
+
+https://github.com/pezmaster31/bamtools/wiki/Mailing-lists
+
+--------------------------------------------------------------------------------
+II. License :
+--------------------------------------------------------------------------------
+
+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 included file LICENSE for details.
+
+--------------------------------------------------------------------------------
+III. Acknowledgements :
+--------------------------------------------------------------------------------
+
+ * 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.
+
+--------------------------------------------------------------------------------
+IV. Contact :
+--------------------------------------------------------------------------------
+
+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