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

I. Introduction
    a. The API
    b. The Toolkit

II. Usage
    a. The API
    b. The Toolkit

III. Contact

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I. Introduction:
BamTools provides both a programmer's API and an end-user's toolkit for handling 
BAM files.  

Ia. The API
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.
 
BamMultiReader is an extra module that allows you to manage multiple open BAM file
for reading. It provides some validation & bookkeeping under the hood to keep all 
files sync'ed for 

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.


Ib. The Toolkit
If you've been using BamTools since the early days, you'll notice that our 'toy' API 
examples (BamConversion, BamDump, and BamTrim) are now gone.  In their place is a set 
of features we hope you find useful.

** More explanation here **

usage: bamtools [--help] COMMAND [ARGS]

Available bamtools commands:
	coverage	Prints coverage statistics from the input BAM file	
	dump		Dump BAM file contents to text output
	header		Prints BAM header information
	index		Generates index for BAM file
	merge		Merge multiple BAM files into single file
	sort		Sorts the BAM file according to some criteria
	stats		Prints some basic statistics from the input BAM file

See 'bamtools help COMMAND' for more information on a specific command.

** Follow-up explanation here **

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II. Usage : 

** General usage information - perhaps explain common terms, point to SAM/BAM spec, etc **


IIa. 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 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. 


IIb. The Toolkit

** More indepth overview for the toolkit commands **

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III. Contact :

Feel free to contact me with any questions, comments, suggestions, bug reports, etc.
  - Derek Barnett

Marth Lab
Biology Dept., Boston College

Email: barnetde@bc.edu  
Project Websites: http://github.com/pezmaster31/bamtools   (ACTIVE SUPPORT)
                  http://sourceforge.net/projects/bamtools (major updates only)