Clarified documentation on BamReader::GetNextAlignmentCore

[bamtools.git] / README

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----------------
-README
-----------------
+--------------------------------------------------------------------------------
+README : BAMTOOLS
+--------------------------------------------------------------------------------
 
+BamTools provides both a programmer's API and an end-user's toolkit for handling
+BAM files.
 
-Significant re-write of BamReader API as of 5/18/2009:
--------------------------------------------------------
-No longer using bgzf.h/.c
-No longer using libbambc.a library
-No longer using STL Utilities
-Minor changes to API syntax in opening BAM files with BamReader - see BamReader.h for details
+I.   Learn More
 
+II.  License
 
-Compile instructions
-----------------------
-Short version:
-See Makefile for compilation example.
+III. Acknowledgements
 
-Longer version:
-Copy BamAlignment.h, BamReader.* and/or BamWriter.* to working directory.
-#include "BamReader.h" and/or "BamWriter.h"
-Use standard compile commands, including the "-lz" parameter to access zlib functionality.
-(Note that "-L. -lbambc" are no longer necessary and WILL CAUSE PROBLEMS for compiler/linker )
+IV.  Contact
 
+--------------------------------------------------------------------------------
+I. Learn More:
+--------------------------------------------------------------------------------
 
-Feel free to email me or pop by my desk with any questions, comments, suggestions, etc.
-  - Derek 
+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