----------------
-README
-----------------
+------------------------------------------------------------
+README : BAMTOOLS
+------------------------------------------------------------
+BamTools: a C++ API & toolkit for reading/writing/manipulating 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. Introduction
+ a. The API
+ b. The Toolkit
+II. Usage
+ a. The API
+ b. The Toolkit
-Compile instructions
-----------------------
-Short version:
-See Makefile for compilation example.
+III. License
-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. Acknowledgements
+V. Contact
-Feel free to email me or pop by my desk with any questions, comments, suggestions, etc.
- - Derek
+------------------------------------------------------------
+
+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 handles writing data to
+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 up for you.
+
+Additional files used by the API:
+ - BamAux.h : contains the common data structures and typedefs used throught the API.
+ - BamIndex.* : implements both the standard BAM format index (".bai") as well as a
+ new BamTools-specific index (".bti").
+ - BGZF.* : contains our implementation of the Broad Institute's BGZF compression format.
+
+
+Ib. The Toolkit:
+
+If you've been using the BamTools since the early days, you'll notice that our 'toy' API
+examples (BamConversion, BamDump, BamTrim,...) are now gone. We dumped these in favor of
+a suite of small utilities that we hope both developers and end-users find useful:
+
+usage: bamtools [--help] COMMAND [ARGS]
+
+Available bamtools commands:
+ convert Converts between BAM and a number of other formats
+ count Prints number of alignments in BAM file(s)
+ coverage Prints coverage statistics from the input BAM file
+ filter Filters BAM file(s) by user-specified criteria
+ header Prints BAM header information
+ index Generates index for BAM file
+ merge Merge multiple BAM files into single file
+ random Select random alignments from existing BAM file(s)
+ sort Sorts the BAM file according to some criteria
+ stats Prints some basic statistics from input BAM file(s)
+
+See 'bamtools help COMMAND' for more information on a specific command.
+
+** Follow-up explanation here **
+
+------------------------------------------------------------
+
+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 API files somewhere the compiler can find them.
+ (i.e. in your project's source tree, or somewhere else in your include path)
+
+ 2 - Import BamTools API with the following lines of code
+ #include "BamReader.h" // or "BamMultiReader.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 MSVC users, I can provide you modified 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 **
+
+------------------------------------------------------------
+
+III. 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 file LICENSE for details.
+
+------------------------------------------------------------
+
+IV. 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.
+
+------------------------------------------------------------
+
+V. 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)
projects / bamtools.git / blobdiff