----------------
-README
-----------------
+------------------------------------------------------------
+README : BAMTOOLS
+------------------------------------------------------------
+BamTools: a C++ API for reading/writing 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
+II. Usage
+III. Contact
+------------------------------------------------------------
-Compile instructions
-----------------------
-Short version:
-See Makefile for compilation example.
-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 )
+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,
+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.
-Feel free to email me or pop by my desk with any questions, comments, suggestions, etc.
- - Derek
+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 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 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 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
+
+http://sourceforge.net/projects/bamtools
projects / bamtools.git / blobdiff