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SAMParser Class Reference

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

#include <mapparser.h>

Inheritance diagram for SAMParser:
Parser

List of all members.

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.

Author:
Adam Roberts
Date:
2011 Artistic License 2.0

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

Definition at line 355 of file mapparser.cpp.


Member Function Documentation

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

An accessor for the header string.

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

Implements Parser.

Definition at line 400 of file mapparser.cpp.


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