Writer Class Reference

The Writer class is an abstract class for implementing a SAMWriter or BAMWriter. More...

#include <mapparser.h>

Inheritance diagram for Writer:

List of all members.

Public Member Functions
virtual	~Writer ()
	Dummy destructor.
virtual void	write_fragment (Fragment &f)=0
	A member function that writes all mappings of the fragment to the ouptut file along with their posterior probabilities in the "XP" field.
Protected Attributes
bool	_sample
	A private bool that specifies if a single alignment should be sampled (true) or all output with their respective posterior probabilities (false).

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Detailed Description

The Writer class is an abstract class for implementing a SAMWriter or BAMWriter.

It writes Fragment objects back to file (in SAM/BAM format) with per-mapping probabilistic assignments, or by sampling a single mapping based on assignment probabilities.

Author:

Adam Roberts

Date:

2011 Artistic License 2.0

Definition at line 99 of file mapparser.h.

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Member Function Documentation

virtual void Writer::write_fragment

(

Fragment &

f

)

[pure virtual]

A member function that writes all mappings of the fragment to the ouptut file along with their posterior probabilities in the "XP" field.

Parameters:

f	the processed Fragment to output.

Implemented in BAMWriter, and SAMWriter.

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

• src/mapparser.h