SAMWriter Class Reference

The SAMWriter class writes Fragment objects back to file in SAM format with per-mapping probabilistic assignments, or by sampling a single mapping based on assignment probabilities. More...

#include <mapparser.h>

Inheritance diagram for SAMWriter:

List of all members.

Public Member Functions
	SAMWriter (std::ostream *out, bool sample)
	SAMWriter constructor stores a pointer to the output stream.
	~SAMWriter ()
	SAMWriter destructor flushes the output stream.
void	write_fragment (Fragment &f)
	A member function that writes the mappings to the output SAM file.

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Detailed Description

The SAMWriter class writes Fragment objects back to file in SAM 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 267 of file mapparser.h.

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Constructor & Destructor Documentation

SAMWriter::SAMWriter	(	std::ostream *	out,
		bool	sample
	)

SAMWriter constructor stores a pointer to the output stream.

Parameters:

out	SAM output stream
sample	specifies if a single alignment should be sampled based on posteriors (true) or all output with their respective posterior probabilities (false).

Definition at line 587 of file mapparser.cpp.

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Member Function Documentation

void SAMWriter::write_fragment

(

Fragment &

f

)

[virtual]

A member function that writes the mappings to the output SAM file.

If _sample is true, a only one alignment is output, otherwise all mappings are output along with their probabilities in the "XP" field.

Parameters:

f	the processed Fragment to output alignments of.

Implements Writer.

Definition at line 595 of file mapparser.cpp.

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

• src/mapparser.h
• src/mapparser.cpp