The BAMParser class fills Fragment objects by parsing an input file in BAM format. More...

#include <mapparser.h>

Inheritance diagram for BAMParser:

Public Member Functions
	BAMParser (BamTools::BamReader *reader)
	BAMParser constructor sets the reader.
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 BAM file.

Detailed Description

The BAMParser class fills Fragment objects by parsing an input file in BAM format.

Definition at line 127 of file mapparser.h.

Constructor & Destructor Documentation

BAMParser::BAMParser ( BamTools::BamReader * reader )

BAMParser constructor sets the reader.

Parameters:

reader a pointer to the BamReader object that will directly parse the BAM file.

Definition at line 239 of file mapparser.cpp.

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

An accessor for the header string.

Implements Parser.

Definition at line 152 of file mapparser.h.

bool BAMParser::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 261 of file mapparser.cpp.

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