eXpress “1.5”
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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. |
The FragHit struct stores the information for a single fragment alignment.
Definition at line 141 of file fragments.h.
FragHit::FragHit | ( | ReadHit * | h | ) | [inline] |
FragHit constructor for single-end read.
h | pointer to the ReadHit struct for the single-end read. |
Definition at line 168 of file fragments.h.
Fraghit constructor for paired-end read.
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.
const ReadHit* FragHit::first_read | ( | ) | const [inline] |
Const accessor for the alignment of the first (or only) read sequenced in the fragment.
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.
Definition at line 349 of file fragments.h.
std::string FragHit::frag_name | ( | ) | const [inline] |
Accessor for 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).
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.
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.
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.
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.
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.
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.
Definition at line 365 of file fragments.h.
HitParams* FragHit::params | ( | ) | [inline] |
Accessor for the hit parameters (likelihood, etc.).
Definition at line 203 of file fragments.h.
const HitParams* FragHit::params | ( | ) | const [inline] |
Const accessor for the hit parameters (likelihood, etc.).
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).
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.
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.
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.
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.
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.
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.
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.
Definition at line 240 of file fragments.h.