template<
AlignmentType TYPE,
typename algorithm_tag,
typename pattern_string,
typename qual_string,
typename text_string,
typename column_type>
struct nvbio::aln::priv::alignment_score_dispatch< EditDistanceAligner< TYPE, algorithm_tag >, pattern_string, qual_string, text_string, column_type >
Calculate the alignment score between a pattern and a text, using the Smith-Waterman algorithm.
- Template Parameters
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TYPE | the alignment type |
pattern_string | pattern string |
quals_string | pattern qualities |
text_string | text string |
column_type | temporary column storage |
Definition at line 62 of file ed_inl.h.
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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) |
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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) |
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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) |
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template<AlignmentType TYPE, typename algorithm_tag , typename pattern_string , typename qual_string , typename text_string , typename column_type >
template<typename sink_type >
NVBIO_FORCEINLINE static NVBIO_HOST_DEVICE bool nvbio::aln::priv::alignment_score_dispatch< EditDistanceAligner< TYPE, algorithm_tag >, pattern_string, qual_string, text_string, column_type >::dispatch |
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const aligner_type |
aligner, |
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const pattern_string |
pattern, |
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const qual_string |
quals, |
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const text_string |
text, |
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const int32 |
min_score, |
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sink_type & |
sink, |
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column_type |
column |
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) |
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inlinestatic |
dispatch scoring across the whole pattern
- Parameters
-
aligner | scoring scheme |
pattern | pattern string (horizontal |
quals | pattern qualities |
text | text string (vertical) |
min_score | minimum score |
sink | output alignment sink |
- Returns
- true iff the minimum score was reached
Definition at line 84 of file ed_inl.h.
template<AlignmentType TYPE, typename algorithm_tag , typename pattern_string , typename qual_string , typename text_string , typename column_type >
template<typename sink_type , typename checkpoint_type >
NVBIO_FORCEINLINE static NVBIO_HOST_DEVICE bool nvbio::aln::priv::alignment_score_dispatch< EditDistanceAligner< TYPE, algorithm_tag >, pattern_string, qual_string, text_string, column_type >::dispatch |
( |
const aligner_type |
aligner, |
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const pattern_string |
pattern, |
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const qual_string |
quals, |
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const text_string |
text, |
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const int32 |
min_score, |
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const uint32 |
window_begin, |
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const uint32 |
window_end, |
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sink_type & |
sink, |
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checkpoint_type |
checkpoint, |
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column_type |
column |
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inlinestatic |
dispatch scoring in a window of the pattern
- Template Parameters
-
checkpoint_type | a class to represent the checkpoint: an array of size equal to the text, that has to provide the const indexing operator[]. |
- Parameters
-
aligner | scoring scheme |
pattern | pattern string (horizontal |
quals | pattern qualities |
text | text string (vertical) |
min_score | minimum score |
sink | output alignment sink |
checkpoint | in/out checkpoint |
- Returns
- true iff the minimum score was reached
Definition at line 123 of file ed_inl.h.
template<AlignmentType TYPE, typename algorithm_tag , typename pattern_string , typename qual_string , typename text_string , typename column_type >
template<typename sink_type >
NVBIO_FORCEINLINE static NVBIO_HOST_DEVICE bool nvbio::aln::priv::alignment_score_dispatch< EditDistanceAligner< TYPE, algorithm_tag >, pattern_string, qual_string, text_string, column_type >::dispatch |
( |
const aligner_type |
aligner, |
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const pattern_string |
pattern, |
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const qual_string |
quals, |
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const text_string |
text, |
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const int32 |
min_score, |
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const uint32 |
window_begin, |
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const uint32 |
window_end, |
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sink_type & |
sink, |
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column_type |
column |
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) |
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inlinestatic |
dispatch scoring in a window of the pattern, retaining the intermediate results in the column vector, essentially used as a continuation
- Parameters
-
aligner | scoring scheme |
pattern | pattern string (horizontal |
quals | pattern qualities |
text | text string (vertical) |
min_score | minimum score |
sink | output alignment sink |
- Returns
- true iff the minimum score was reached
Definition at line 158 of file ed_inl.h.