The FragHit struct stores the information for a single fragment alignment. More...

#include <fragments.h>

Public Member Functions
	FragHit (ReadHit *h)
	FragHit constructor for single-end read.
	FragHit (ReadHit l, ReadHit r)
	Fraghit constructor for paired-end read.
std::string	frag_name () const
	Accessor for the name of the fragment.
HitParams *	params ()
	Accessor for the hit parameters (likelihood, etc.).
const HitParams *	params () const
	Const accessor for the hit parameters (likelihood, etc.).
Target *	target () const
	Accessor for a pointer to the Target object the fragment is aligned to.
void	target (Target *target)
	Mutator for a pointer to the Target object the fragment is aligned to.
const std::vector< const Target * > *	neighbors () const
	Accessor for a pointer to the vector of neighbors to the target.
void	neighbors (const std::vector< const Target * > &neighbors)
	Mutator for a vector of neighbors to the target.
TargID	target_id () const
	Accessor for the ID of the target the fragment is aligned to.
size_t	left () const
	Accessor for the leftmost position aligned to (0-based).
size_t	right () const
	Accessor for one position past the rightmost position aligned to (0-based).
size_t	length () const
	Accessor for the length of the fragment alignment.
const ReadHit *	left_read () const
	Const accessor for the alignment of the read at the leftmost (5') end of the fragment in target coordinates or NULL if it was not sequenced.
const ReadHit *	right_read () const
	Const accessor for the alignment of the read at the rightmost (3') end of the fragment in target coordinates or NULL if it was not sequenced.
const ReadHit *	first_read () const
	Const accessor for the alignment of the first (or only) read sequenced in the fragment.
const ReadHit *	second_read () const
	Const accessor for the alignment of the second read sequenced in the fragment.
ReadHit *	left_read ()
	Accessor for the alignment of the read at the leftmost (5') end of the fragment in target coordinates or NULL if it was not sequenced.
ReadHit *	right_read ()
	Accessor for the alignment of the read at the rightmost (3') end of the fragment in target coordinates or NULL if it was not sequenced.
ReadHit *	first_read ()
	Accessor for the alignment of the first (or only) read sequenced in the fragment.
ReadHit *	second_read ()
	Accessor for the alignment of the second read sequenced in the fragment.
PairStatus	pair_status () const
	A member function returning whether the mapping is PAIRED, LEFT_ONLY, or RIGHT_ONLY, as defined in the PairStatus enum definition.

Detailed Description

The FragHit struct stores the information for a single fragment alignment.

Author:: Adam Roberts

Date:: 2011 Artistic License 2.0

Definition at line 141 of file fragments.h.

Constructor & Destructor Documentation

FragHit::FragHit ( ReadHit * h ) [inline]

FragHit constructor for single-end read.

Parameters:

h	pointer to the ReadHit struct for the single-end read.

Definition at line 168 of file fragments.h.

FragHit::FragHit	(	ReadHit *	l,
		ReadHit *	r
	)		`[inline]`

Fraghit constructor for paired-end read.

Parameters:

l	pointer to the ReadHit struct for the upstream (left) read.
r	pointer to the ReadHit struct for the downstream (right) read.

Definition at line 180 of file fragments.h.

Member Function Documentation

const ReadHit* FragHit::first_read ( ) const [inline]

Const accessor for the alignment of the first (or only) read sequenced in the fragment.

Returns:: A const pointer to the alignment of the first read.

Definition at line 307 of file fragments.h.

ReadHit* FragHit::first_read ( ) [inline]

Accessor for the alignment of the first (or only) read sequenced in the fragment.

Returns:: A pointer to the alignment of the first read.

Definition at line 349 of file fragments.h.

std::string FragHit::frag_name ( ) const [inline]

Accessor for the name of the fragment.

Returns:: The name of the fragment.

Definition at line 192 of file fragments.h.

size_t FragHit::left ( ) const [inline]

Accessor for the leftmost position aligned to (0-based).

Returns:: The leftmost position aligned to in the target.

Definition at line 251 of file fragments.h.

ReadHit* FragHit::left_read ( ) [inline]

Accessor for the alignment of the read at the leftmost (5') end of the fragment in target coordinates or NULL if it was not sequenced.

Returns:: A pointer to the 5' read alignment.

Definition at line 333 of file fragments.h.

const ReadHit* FragHit::left_read ( ) const [inline]

Const accessor for the alignment of the read at the leftmost (5') end of the fragment in target coordinates or NULL if it was not sequenced.

Returns:: A const pointer to the 5' read alignment.

Definition at line 285 of file fragments.h.

size_t FragHit::length ( ) const [inline]

Accessor for the length of the fragment alignment.

Returns 0 if the fragment is single-end.

Returns:: Length of fragment mapping.

Definition at line 274 of file fragments.h.

const std::vector<const Target*>* FragHit::neighbors ( ) const [inline]

Accessor for a pointer to the vector of neighbors to the target.

Experimental.

Returns:: A pointer to the vector of neighbors.

Definition at line 228 of file fragments.h.

void FragHit::neighbors ( const std::vector< const Target * > & neighbors ) [inline]

Mutator for a vector of neighbors to the target.

Experimental.

Parameters:

neighbors a vector of neighbors to the target.

Definition at line 233 of file fragments.h.

PairStatus FragHit::pair_status ( ) const [inline]

A member function returning whether the mapping is PAIRED, LEFT_ONLY, or RIGHT_ONLY, as defined in the PairStatus enum definition.

Returns:: The pair status of the mapping.

Definition at line 365 of file fragments.h.

HitParams* FragHit::params ( ) [inline]

Accessor for the hit parameters (likelihood, etc.).

Returns:: A pointer to the hit parameters.

Definition at line 203 of file fragments.h.

const HitParams* FragHit::params ( ) const [inline]

Const accessor for the hit parameters (likelihood, etc.).

Returns:: A const pointer to the hit parameters.

Definition at line 208 of file fragments.h.

size_t FragHit::right ( ) const [inline]

Accessor for one position past the rightmost position aligned to (0-based).

Returns:: One past the rightmost position aligned to in the target.

Definition at line 262 of file fragments.h.

ReadHit* FragHit::right_read ( ) [inline]

Accessor for the alignment of the read at the rightmost (3') end of the fragment in target coordinates or NULL if it was not sequenced.

Returns:: A pointer to the 3' read alignment.

Definition at line 341 of file fragments.h.

const ReadHit* FragHit::right_read ( ) const [inline]

Const accessor for the alignment of the read at the rightmost (3') end of the fragment in target coordinates or NULL if it was not sequenced.

Returns:: A const pointer to the 3' read alignment.

Definition at line 296 of file fragments.h.

ReadHit* FragHit::second_read ( ) [inline]

Accessor for the alignment of the second read sequenced in the fragment.

Returns NULL if single-end.

Returns:: A pointer to the alignment of the second read.

Definition at line 357 of file fragments.h.

const ReadHit* FragHit::second_read ( ) const [inline]

Const accessor for the alignment of the second read sequenced in the fragment.

Returns NULL if single-end.

Returns:: A const pointer to the alignment of the second read.

Definition at line 319 of file fragments.h.

Target* FragHit::target ( ) const [inline]

Accessor for a pointer to the Target object the fragment is aligned to.

Returns:: A pointer to the Target aligned to.

Definition at line 213 of file fragments.h.

void FragHit::target ( Target * target ) [inline]

Mutator for a pointer to the Target object the fragment is aligned to.

Parameters:

target a pointer to the Target aligned to.

Definition at line 220 of file fragments.h.

TargID FragHit::target_id ( ) const [inline]

Accessor for the ID of the target the fragment is aligned to.

Returns:: The ID of the target aligned to.

Definition at line 240 of file fragments.h.

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

src/fragments.h

FragHit Class Reference

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation