Parser Class Reference

The Parser class is an abstract class for implementing a SAMParser or BAMParser. More...

#include <mapparser.h>

Inheritance diagram for Parser:

List of all members.

Public Member Functions
virtual	~Parser ()
	Dummy destructor.
virtual const std::string	header () const =0
	An accessor for the SAM header string.
const TransIndex &	targ_index () const
	An accessor for the target name to index map.
const TransIndex &	targ_lengths () const
	An accessor for the target-to-length map.
virtual bool	next_fragment (Fragment &f)=0
	A member function that loads all mappings of the next fragment into the given Fragment object.
virtual void	reset ()=0
	A member function that resets the parser and rewinds to the beginning of the input.
Protected Attributes
TransIndex	_targ_index
	The private target-to-index map.
TransIndex	_targ_lengths
	The private target-to-length map.
ReadHit *	_read_buff
	A private pointer to the current/last read mapping being parsed.

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Detailed Description

The Parser class is an abstract class for implementing a SAMParser or BAMParser.

It fills Fragment objects by parsing an input file in SAM/BAM format.

Author:

Adam Roberts

Date:

2011 Artistic License 2.0

Definition at line 39 of file mapparser.h.

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Member Function Documentation

virtual const std::string Parser::header

(

)

const [pure virtual]

An accessor for the SAM header string.

Returns:

The SAM header string.

Implemented in BAMParser, and SAMParser.

virtual bool Parser::next_fragment

(

Fragment &

f

)

[pure 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.

Returns:

True iff more reads remain in the SAM/BAM file/stream.

Implemented in BAMParser, and SAMParser.

const TransIndex& Parser::targ_index

(

)

const [inline]

An accessor for the target name to index map.

Returns a reference that does not outlive this.

Returns:

Reference to the target-to-index map.

Definition at line 69 of file mapparser.h.

const TransIndex& Parser::targ_lengths

(

)

const [inline]

An accessor for the target-to-length map.

Returns a reference that does not outlive this.

Returns:

Reference to the target-to-length map.

Definition at line 75 of file mapparser.h.

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

• src/mapparser.h