X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=README;h=498f4be06dc0ecc00162c43cdaa65841cea5dff8;hb=1a0f5104b8e573a22be5a57ea861129b5e86ad22;hp=53d80c02d88b254fbd0baa345da71c58b6a8d977;hpb=1b19b64a28c1a892f2fcbb00b111853c5e8a2f8e;p=bamtools.git diff --git a/README b/README index 53d80c0..498f4be 100644 --- a/README +++ b/README @@ -1,130 +1,60 @@ ------------------------------------------------------------- +-------------------------------------------------------------------------------- README : BAMTOOLS ------------------------------------------------------------- +-------------------------------------------------------------------------------- -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