AMOS::BaseStats_t Class Reference

Maintains statistics the Column_t about reads which share the same base at the current position. More...

#include <ContigIterator_AMOS.hh>

List of all members.

Public Member Functions
	BaseStats_t (char base)
	The base this BaseStats_t will represent.
void	addRead (TiledReadList_t::const_iterator tile, Pos_t gindex)
	Used to add a read to the BaseStats_t.
Public Attributes
char	m_base
	The base this BaseStats_t represents.
int	m_cumqv
	The cumulative quality value of the reads that tile the current position that are m_base.
int	m_maxqv
	The maximum quality value of the reads that tile the current position that are m_base.
std::vector< TiledReadList_t::const_iterator >	m_reads
	A vector of reads that tile the current position that are m_base.

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Detailed Description

Maintains statistics the Column_t about reads which share the same base at the current position.

Reads that agree at the current contig position are stored in the same BaseStats_t object. The object maintains a list of reads that agree, and some general statistics on the bases that tile that position.

Definition at line 128 of file ContigIterator_AMOS.hh.

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Constructor & Destructor Documentation

BaseStats_t::BaseStats_t

(

char

base

)

The base this BaseStats_t will represent.

Definition at line 190 of file ContigIterator_AMOS.cc.

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Member Function Documentation

void BaseStats_t::addRead	(	TiledReadList_t::const_iterator	tile,
		Pos_t	gindex
	)

Used to add a read to the BaseStats_t.

Definition at line 194 of file ContigIterator_AMOS.cc.

References m_cumqv, m_maxqv, and m_reads.

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Member Data Documentation

char AMOS::BaseStats_t::m_base

The base this BaseStats_t represents.

Definition at line 135 of file ContigIterator_AMOS.hh.

int AMOS::BaseStats_t::m_cumqv

The cumulative quality value of the reads that tile the current position that are m_base.

Definition at line 138 of file ContigIterator_AMOS.hh.

Referenced by addRead(), and AMOS::BaseStatsCmp::operator()().

int AMOS::BaseStats_t::m_maxqv

The maximum quality value of the reads that tile the current position that are m_base.

Definition at line 141 of file ContigIterator_AMOS.hh.

Referenced by addRead(), and AMOS::BaseStatsCmp::operator()().

std::vector<TiledReadList_t::const_iterator> AMOS::BaseStats_t::m_reads

A vector of reads that tile the current position that are m_base.

Definition at line 144 of file ContigIterator_AMOS.hh.

Referenced by addRead(), and AMOS::BaseStatsCmp::operator()().

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

• ContigIterator_AMOS.hh
• ContigIterator_AMOS.cc

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