BAMWriter Class Reference

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

#include <mapparser.h>

Inheritance diagram for BAMWriter:

List of all members.

Public Member Functions
	BAMWriter (BamTools::BamWriter *writer, bool sample)
	BAMWriter constructor stores a pointer to the BamTools::BamWriter object that will directly write to the BAM file.
	~BAMWriter ()
	BAMWriter destructor closes the BamTools::BamWriter object.
void	write_fragment (Fragment &f)
	A member function that writes the mappings to the output BAM file.

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Detailed Description

The BAMWriter class writes Fragment objects back to file in 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 226 of file mapparser.h.

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Constructor & Destructor Documentation

BAMWriter::BAMWriter	(	BamTools::BamWriter *	writer,
		bool	sample
	)

BAMWriter constructor stores a pointer to the BamTools::BamWriter object that will directly write to the BAM file.

Parameters:

writer	pointer to the BamTools::BamWriter objected assocaited with the output BAM file.
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 550 of file mapparser.cpp.

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Member Function Documentation

void BAMWriter::write_fragment

(

Fragment &

f

)

[virtual]

A member function that writes the mappings to the output BAM 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 559 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