NVBIO
|
Calculate the alignment score between a pattern and a text, using the Smith-Waterman algorithm.
TYPE | the alignment type |
pattern_string | pattern string |
quals_string | pattern qualities |
text_string | text string |
column_type | temporary column storage |
Definition at line 1313 of file hamming_inl.h.
#include <hamming_inl.h>
Public Types | |
typedef HammingDistanceAligner < TYPE, scoring_type, algorithm_tag > | aligner_type |
Static Public Methods | |
template<typename sink_type > | |
NVBIO_FORCEINLINE static NVBIO_HOST_DEVICE bool | dispatch (const aligner_type aligner, const pattern_string pattern, const qual_string quals, const text_string text, const int32 min_score, sink_type &sink, column_type column) |
template<typename sink_type , typename checkpoint_type > | |
NVBIO_FORCEINLINE static NVBIO_HOST_DEVICE bool | dispatch (const aligner_type aligner, const pattern_string pattern, const qual_string quals, const text_string text, const int32 min_score, const uint32 window_begin, const uint32 window_end, sink_type &sink, checkpoint_type checkpoint, column_type column) |
template<typename sink_type > | |
NVBIO_FORCEINLINE static NVBIO_HOST_DEVICE bool | dispatch (const aligner_type aligner, const pattern_string pattern, const qual_string quals, const text_string text, const int32 min_score, const uint32 window_begin, const uint32 window_end, sink_type &sink, column_type column) |
typedef HammingDistanceAligner<TYPE,scoring_type,algorithm_tag> nvbio::aln::priv::alignment_score_dispatch< HammingDistanceAligner< TYPE, scoring_type, algorithm_tag >, pattern_string, qual_string, text_string, column_type >::aligner_type |
Definition at line 1320 of file hamming_inl.h.
|
inlinestatic |
dispatch scoring across the whole pattern
aligner | scoring scheme |
pattern | pattern string (horizontal |
quals | pattern qualities |
text | text string (vertical) |
min_score | minimum score |
sink | output alignment sink |
column | temporary column storage |
Definition at line 1336 of file hamming_inl.h.
|
inlinestatic |
dispatch scoring in a window of the pattern
checkpoint_type | a class to represent the checkpoint: an array of size equal to the text, that has to provide the const indexing operator[]. |
aligner | scoring scheme |
pattern | pattern string (horizontal |
quals | pattern qualities |
text | text string (vertical) |
min_score | minimum score |
sink | output alignment sink |
column | temporary column storage |
Definition at line 1375 of file hamming_inl.h.
|
inlinestatic |
dispatch scoring in a window of the pattern, retaining the intermediate results in the column vector, essentially used as a continuation
aligner | scoring scheme |
pattern | pattern string (horizontal) |
quals | pattern qualities |
text | text string (vertical) |
min_score | minimum score |
sink | output alignment sink |
column | temporary column storage |
Definition at line 1411 of file hamming_inl.h.