Updated README

[bamtools.git] / README

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----------------
-README
-----------------
+------------------------------------------------------------
+README : BAMTOOLS
+------------------------------------------------------------
 
-Copy the 4 header files (*.h) and the library file (libbambc.a) to your directory.
+BamTools: a C++ API for reading/writing BAM files.
 
-When you compile your program, add this to the g++ command:
+I.   Introduction
+II.  Usage
+III. Contact
 
-           -lz -L. -lbambc
+------------------------------------------------------------
 
-and you should be good to go.  (Those are lower case l's, as in 'lion'.)
+
+I. Introduction:
+
+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.
+
+BGZF.h & BGZF.cpp contain our implementation of the Broad Institute's 
+BGZF compression format.
+
+BamConversion, BamDump, and BamTrim are 3 'toy' examples on how the API can be used.
+
+------------------------------------------------------------
+
+Usage : 
+
+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. 
+
+------------------------------------------------------------
+
+Contact :
+
+Feel free to contact me with any questions, comments, suggestions, bug reports, etc.
+  - Derek Barnett
+  
+http://sourceforge.net/projects/bamtools