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+--------------------------------------------------------------------------------
README : BAMTOOLS
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+--------------------------------------------------------------------------------
-BamTools: a C++ API & toolkit for reading/writing/manipulating BAM files.
+BamTools provides both a programmer's API and an end-user's toolkit for handling
+BAM files.
-I. Introduction
- a. The API
- b. The Toolkit
+I. Learn More
-II. Usage
- a. The API
- b. The Toolkit
+II. License
-III. License
+III. Acknowledgements
-IV. Acknowledgements
+IV. Contact
-V. Contact
+--------------------------------------------------------------------------------
+I. Learn More:
+--------------------------------------------------------------------------------
-------------------------------------------------------------
+Installation steps, tutorial, API documentation, etc. are all now available
+through the BamTools project wiki:
-I. Introduction:
+https://github.com/pezmaster31/bamtools/wiki
-BamTools provides both a programmer's API and an end-user's toolkit for handling
-BAM files.
+Join the mailing list(s) to stay informed of updates or get involved with
+contributing:
+https://github.com/pezmaster31/bamtools/wiki/Mailing-lists
-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 :
+--------------------------------------------------------------------------------
+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 file LICENSE for details.
+Copyright (c) 2009-2010 Derek Barnett, Erik Garrison, Gabor Marth,
+ Michael Stromberg
-------------------------------------------------------------
+See included file LICENSE for details.
-IV. Acknowledgements :
+--------------------------------------------------------------------------------
+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.
-------------------------------------------------------------
-
-V. Contact :
+--------------------------------------------------------------------------------
+IV. Contact :
+--------------------------------------------------------------------------------
-Feel free to contact me with any questions, comments, suggestions, bug reports, etc.
- - Derek Barnett
+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)
-
+Email: derekwbarnett@gmail.com
+Project Website: http://github.com/pezmaster31/bamtools
projects / bamtools.git / blobdiff