AMOS::TiledRead_t Class Reference

A read within a contig "rendered" with gaps inserted. More...

#include <ContigIterator_AMOS.hh>

List of all members.

Public Member Functions
	TiledRead_t (Tile_t tile, Read_t red, int readidx)
	The tile information is used to render the sequence from the read. readidx is an index to assign.
char	base (Pos_t gindex) const
	Returns the base at a given gapped consensus position or ' ' if outside the tiled range.
int	qv (Pos_t gindex) const
	Returns the qv at a given gapped consensus position or -1 if outside the tiled range.
Public Attributes
int32_t	m_readidx
	Callee assigned index for read.
Pos_t	m_loffset
	Left offset of the read in the contig.
Pos_t	m_roffset
	Right offset of the read in the contig.
bool	m_isRC
	Boolean indicating if the read has been reversed.
ID_t	m_fragid
	iid of the read's fragment
ID_t	m_iid
	iid of the read
std::string	m_eid
	eid of the read

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Detailed Description

A read within a contig "rendered" with gaps inserted.

An enhanced version of a read object which with the sequence and quality values rendered with the gaps inserted.

Definition at line 35 of file ContigIterator_AMOS.hh.

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Constructor & Destructor Documentation

TiledRead_t::TiledRead_t	(	Tile_t	tile,
		Read_t	red,
		int	readidx
	)

The tile information is used to render the sequence from the read. readidx is an index to assign.

Definition at line 9 of file ContigIterator_AMOS.cc.

References AMOS_THROW_ARGUMENT, AMOS::Tile_t::gaps, AMOS::IBankable_t::getEID(), AMOS::Tile_t::getGappedLength(), AMOS::Range_t::isReverse(), m_isRC, m_loffset, m_roffset, AMOS::Tile_t::offset, and AMOS::Tile_t::range.

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Member Function Documentation

char AMOS::TiledRead_t::base

(

Pos_t

gindex

)

const [inline]

Returns the base at a given gapped consensus position or ' ' if outside the tiled range.

Definition at line 43 of file ContigIterator_AMOS.hh.

References m_loffset, and m_roffset.

int AMOS::TiledRead_t::qv

(

Pos_t

gindex

)

const [inline]

Returns the qv at a given gapped consensus position or -1 if outside the tiled range.

Definition at line 50 of file ContigIterator_AMOS.hh.

References m_loffset, m_roffset, and AMOS::MIN_QUALITY.

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Member Data Documentation

std::string AMOS::TiledRead_t::m_eid

eid of the read

Definition at line 75 of file ContigIterator_AMOS.hh.

ID_t AMOS::TiledRead_t::m_fragid

iid of the read's fragment

Definition at line 69 of file ContigIterator_AMOS.hh.

ID_t AMOS::TiledRead_t::m_iid

iid of the read

Definition at line 72 of file ContigIterator_AMOS.hh.

bool AMOS::TiledRead_t::m_isRC

Boolean indicating if the read has been reversed.

Definition at line 66 of file ContigIterator_AMOS.hh.

Referenced by TiledRead_t().

Pos_t AMOS::TiledRead_t::m_loffset

Left offset of the read in the contig.

Definition at line 60 of file ContigIterator_AMOS.hh.

Referenced by base(), qv(), and TiledRead_t().

int32_t AMOS::TiledRead_t::m_readidx

Callee assigned index for read.

Definition at line 57 of file ContigIterator_AMOS.hh.

Pos_t AMOS::TiledRead_t::m_roffset

Right offset of the read in the contig.

Definition at line 63 of file ContigIterator_AMOS.hh.

Referenced by base(), qv(), and TiledRead_t().

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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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