Updated README

[bamtools.git] / README

diff --git a/README b/README
index 92f88d152efd75d0fb237577f3e14758db400beb..dc24cbbee8a64c563a20c886300b7eca3f98f18b 100644 (file)
--- a/README
+++ b/README
@@ -4,32 +4,52 @@ README : BAMTOOLS
 
 BamTools: a C++ API for reading/writing BAM files.
 
 
 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
 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.
 
  
 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.
 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;
        
 
     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 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
   
 Feel free to contact me with any questions, comments, suggestions, bug reports, etc.
   - Derek Barnett