Clarified documentation on BamReader::GetNextAlignmentCore

[bamtools.git] / README

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-------------------------------------------------------------
-    README
-------------------------------------------------------------
-
-BamTools: a C++ API for reading/writing 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.
-
-------------------------------------------------------------
-
-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 source directory, or somewhere in 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 'lion') to access ZLIB compression library
-
-See any included programs and Makefile for more specific compiling/usage examples.
-See documentation & comments in header files for API details. 
-
-------------------------------------------------------------
-
-Feel free to contact me with any questions, comments, suggestions, bug reports, etc.
-  - Derek Barnett
-  
-http://sourceforge.net/projects/bamtools
+--------------------------------------------------------------------------------
+README : BAMTOOLS
+--------------------------------------------------------------------------------
+
+BamTools provides both a programmer's API and an end-user's toolkit for handling
+BAM files.
+
+I.   Learn More
+
+II.  License
+
+III. Acknowledgements
+
+IV.  Contact
+
+--------------------------------------------------------------------------------
+I. Learn More:
+--------------------------------------------------------------------------------
+
+Installation steps, tutorial, API documentation, etc. are all now available 
+through the BamTools project wiki:
+
+https://github.com/pezmaster31/bamtools/wiki
+
+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