eXpress “1.5”

BAMParser Class Reference

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

#include <mapparser.h>

Inheritance diagram for BAMParser:
Parser

List of all members.

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.

Author:
Adam Roberts
Date:
2011 Artistic License 2.0

Definition at line 127 of file mapparser.h.


Constructor & Destructor Documentation

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

BAMParser constructor sets the reader.

Parameters:
readera pointer to the BamReader object that will directly parse the BAM file.

Definition at line 239 of file mapparser.cpp.


Member Function Documentation

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

An accessor for the header string.

Returns:
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:
fthe empty Fragment to add mappings to.
Returns:
True iff more reads remain in the BAM file/stream.

Implements Parser.

Definition at line 261 of file mapparser.cpp.


The documentation for this class was generated from the following files:
 All Classes Functions Variables