Read Me

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README : BAMTOOLS
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BamTools: a C++ API for reading/writing BAM files.

I.   Introduction
II.  Usage
III. Contact

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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.

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II. 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. 

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III. Contact :

Feel free to contact me with any questions, comments, suggestions, bug reports, etc.
  - Derek Barnett
  
http://sourceforge.net/projects/bamtools