BamTools: a C++ API for reading/writing BAM files.
+I. Introduction
+II. Usage
+III. Contact
+
+------------------------------------------------------------
+
+
+I. Introduction:
+
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.
+files. BamReader provides an interface for random-access (jumping) in a BAM file,
+as well as generating BAM index files.
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.
+
+BamConversion, BamDump, and BamTrim are 3 'toy' examples on how the API can be used.
+
------------------------------------------------------------
+Usage :
+
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 source directory, or somewhere in include path)
+ (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 'lion') to access ZLIB compression library
+ 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 documentation & comments in header files for API details.
+See comments in the header files for more detailed API documentation.
------------------------------------------------------------
+Contact :
+
Feel free to contact me with any questions, comments, suggestions, bug reports, etc.
- Derek Barnett
projects / bamtools.git / blobdiff