The SAMParser class fills Fragment objects by parsing an input in SAM format. More...

#include <mapparser.h>

Inheritance diagram for SAMParser:

Public Member Functions
	SAMParser (std::istream *in)
	SAMParser constructor removes the header and parses the first line to start the first Fragment.
const std::string	header () const
	An accessor for the header string.
bool	next_fragment (Fragment &f)
	A member function that loads all mappings of the next fragment into the given Fragment object.
void	reset ()
	A member function that resets the parser and rewinds to the beginning of the SAM file.

Detailed Description

The SAMParser class fills Fragment objects by parsing an input in SAM format.

The input may come from a file or stdin.

Definition at line 174 of file mapparser.h.

Constructor & Destructor Documentation

SAMParser::SAMParser ( std::istream * in )

SAMParser constructor removes the header and parses the first line to start the first Fragment.

Parameters:

in	the input stream in SAM format, which may be a file or stdin.

Definition at line 355 of file mapparser.cpp.

const std::string SAMParser::header ( ) const [inline, virtual]

An accessor for the header string.

Implements Parser.

Definition at line 203 of file mapparser.h.

bool SAMParser::next_fragment ( Fragment & f ) [virtual]

A member function that loads all mappings of the next fragment into the given Fragment object.

Parameters:

f	the empty Fragment to add mappings to.

Implements Parser.

Definition at line 400 of file mapparser.cpp.

The documentation for this class was generated from the following files: