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5 BamTools: a C++ API & toolkit for reading/writing/manipulating BAM files.
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20 BamTools provides both a programmer's API and an end-user's toolkit for handling
24 The API consists of 2 main modules - BamReader and BamWriter. As you would expect,
25 BamReader provides read-access to BAM files, while BamWriter does the writing of BAM
26 files. BamReader provides an interface for random-access (jumping) in a BAM file,
27 as well as generating BAM index files.
29 BamMultiReader is an extra module that allows you to manage multiple open BAM file
30 for reading. It provides some validation & bookkeeping under the hood to keep all
33 An additional file, BamAux.h, is included as well.
34 This file contains the common data structures and typedefs used throught the API.
36 BGZF.h & BGZF.cpp contain our implementation of the Broad Institute's
37 BGZF compression format.
41 If you've been using BamTools since the early days, you'll notice that our 'toy' API
42 examples (BamConversion, BamDump, and BamTrim) are now gone. In their place is a set
43 of features we hope you find useful.
45 ** More explanation here **
47 usage: bamtools [--help] COMMAND [ARGS]
49 Available bamtools commands:
50 convert Converts between BAM and a number of other formats
51 count Prints number of alignments in BAM file
52 coverage Prints coverage statistics from the input BAM file
53 filter Filters BAM file(s) by user-specified criteria
54 header Prints BAM header information
55 index Generates index for BAM file
56 merge Merge multiple BAM files into single file
57 sam Prints the BAM file in SAM (text) format
58 sort Sorts the BAM file according to some criteria
59 stats Prints some basic statistics from the input BAM file
61 See 'bamtools help COMMAND' for more information on a specific command.
63 ** Follow-up explanation here **
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69 ** General usage information - perhaps explain common terms, point to SAM/BAM spec, etc **
74 To use this API, you simply need to do 3 things:
76 1 - Drop the BamTools files somewhere the compiler can find them.
77 (i.e. in your source tree, or somewhere else in your include path)
79 2 - Import BamTools API with the following lines of code
80 #include "BamReader.h" // as needed
81 #include "BamWriter.h" // as needed
82 using namespace BamTools;
84 3 - Compile with '-lz' ('l' as in Lima) to access ZLIB compression library
85 (For VS users, I can provide you zlib headers - just contact me).
87 See any included programs and Makefile for more specific compiling/usage examples.
88 See comments in the header files for more detailed API documentation.
93 ** More indepth overview for the toolkit commands **
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99 Feel free to contact me with any questions, comments, suggestions, bug reports, etc.
103 Biology Dept., Boston College
105 Email: barnetde@bc.edu
106 Project Websites: http://github.com/pezmaster31/bamtools (ACTIVE SUPPORT)
107 http://sourceforge.net/projects/bamtools (major updates only)