NVBIO
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Groups Pages
Namespaces | Classes | Functions
nvbio::aln::priv Namespace Reference

Namespaces

 banded
 

Classes

struct  alignment_score_dispatch
 
struct  alignment_checkpointed_dispatch
 
struct  banded_alignment_score_dispatch
 
struct  banded_alignment_checkpointed_dispatch
 
struct  Reference_cache
 
struct  Reference_cache< 15u >
 
struct  Reference_cache< 7u >
 
struct  Reference_cache< 5u >
 
struct  Reference_cache< 3u >
 
struct  AlignmentStream
 
struct  alignment_score_dispatch< EditDistanceAligner< TYPE, algorithm_tag >, pattern_string, qual_string, text_string, column_type >
 
struct  alignment_checkpointed_dispatch< CHECKPOINTS, EditDistanceAligner< TYPE >, pattern_string, qual_string, text_string, column_type >
 
struct  EditDistanceSWScheme
 
struct  gotoh_use_vectorization
 
struct  gotoh_use_vectorization< vector_view< T * > >
 
struct  gotoh_use_vectorization< vector_view< const T * > >
 
struct  GotohScoringContext
 
struct  GotohCheckpointedScoringContext
 
struct  GotohCheckpointContext
 
struct  GotohSubmatrixContext
 
struct  gotoh_alignment_score_dispatch
 
struct  gotoh_alignment_score_dispatch< BAND_LEN, TYPE, PatternBlockingTag, symbol_type >
 
struct  gotoh_alignment_score_dispatch< BAND_LEN, TYPE, TextBlockingTag, symbol_type >
 
struct  gotoh_bandlen_selector
 
struct  gotoh_bandlen_selector< TYPE, DIM, simd4u8 >
 
struct  alignment_score_dispatch< GotohAligner< TYPE, scoring_type, algorithm_tag >, pattern_string, qual_string, text_string, column_type >
 
struct  alignment_checkpointed_dispatch< CHECKPOINTS, GotohAligner< TYPE, scoring_type >, pattern_string, qual_string, text_string, column_type >
 
struct  HammingScoringContext
 
struct  HammingCheckpointedScoringContext
 
struct  HammingCheckpointContext
 
struct  HammingSubmatrixContext
 
struct  hamming_alignment_score_dispatch
 
struct  hamming_alignment_score_dispatch< BAND_LEN, TYPE, PatternBlockingTag, symbol_type >
 
struct  hamming_alignment_score_dispatch< BAND_LEN, TYPE, TextBlockingTag, symbol_type >
 
struct  hamming_bandlen_selector
 
struct  hamming_bandlen_selector< TYPE, DIM, simd4u8 >
 
struct  alignment_score_dispatch< HammingDistanceAligner< TYPE, scoring_type, algorithm_tag >, pattern_string, qual_string, text_string, column_type >
 
struct  alignment_checkpointed_dispatch< CHECKPOINTS, HammingDistanceAligner< TYPE, scoring_type >, pattern_string, qual_string, text_string, column_type >
 
struct  MyersBitVectors
 
struct  MyersBitVectors< 2 >
 
struct  MyersBitVectors< 4 >
 
struct  MyersBitVectors< 5 >
 
struct  SWScoringContext
 
struct  SWCheckpointedScoringContext
 
struct  SWCheckpointContext
 
struct  SWSubmatrixContext
 
struct  sw_alignment_score_dispatch
 
struct  sw_alignment_score_dispatch< BAND_LEN, TYPE, PatternBlockingTag, symbol_type >
 
struct  sw_alignment_score_dispatch< BAND_LEN, TYPE, TextBlockingTag, symbol_type >
 
struct  sw_bandlen_selector
 
struct  sw_bandlen_selector< TYPE, DIM, simd4u8 >
 
struct  alignment_score_dispatch< SmithWatermanAligner< TYPE, scoring_type, algorithm_tag >, pattern_string, qual_string, text_string, column_type >
 
struct  alignment_checkpointed_dispatch< CHECKPOINTS, SmithWatermanAligner< TYPE, scoring_type >, pattern_string, qual_string, text_string, column_type >
 
struct  alignment_result
 

Functions

template<uint32 BAND_LEN, AlignmentType TYPE, typename pattern_type , typename qual_type , typename text_type , typename sink_type >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE bool 
banded_alignment_score (const EditDistanceAligner< TYPE > &aligner, pattern_type pattern, qual_type quals, text_type text, const int32 min_score, sink_type &sink)
 
template<uint32 BAND_LEN, AlignmentType TYPE, typename pattern_type , typename qual_type , typename text_type , typename sink_type , typename checkpoint_type >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE bool 
banded_alignment_score (const EditDistanceAligner< TYPE > &aligner, pattern_type pattern, qual_type quals, text_type text, const int32 min_score, const uint32 window_begin, const uint32 window_end, sink_type &sink, checkpoint_type checkpoint)
 
template<uint32 BAND_LEN, uint32 CHECKPOINTS, AlignmentType TYPE, typename pattern_type , typename qual_type , typename text_type , typename sink_type , typename checkpoint_type >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE bool 
banded_alignment_checkpoints (const EditDistanceAligner< TYPE > &aligner, pattern_type pattern, qual_type quals, text_type text, const int32 min_score, sink_type &sink, checkpoint_type checkpoints)
 
template<uint32 BAND_LEN, uint32 CHECKPOINTS, AlignmentType TYPE, typename pattern_string , typename qual_string , typename text_string , typename checkpoint_type , typename submatrix_type >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE uint32 
banded_alignment_submatrix (const EditDistanceAligner< TYPE > &aligner, pattern_string pattern, qual_string quals, text_string text, const int32 min_score, checkpoint_type checkpoints, const uint32 checkpoint_id, submatrix_type submatrix)
 
template<uint32 BAND_LEN, uint32 CHECKPOINTS, AlignmentType TYPE, typename checkpoint_type , typename submatrix_type , typename backtracer_type >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE bool 
banded_alignment_traceback (const EditDistanceAligner< TYPE > &aligner, checkpoint_type checkpoints, const uint32 checkpoint_id, submatrix_type submatrix, const uint32 submatrix_height, uint8 &state, uint2 &sink, backtracer_type &backtracer)
 
template<uint32 CHECKPOINTS, AlignmentType TYPE, typename checkpoint_type , typename submatrix_type , typename backtracer_type >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE bool 
alignment_traceback (const EditDistanceAligner< TYPE > aligner, checkpoint_type checkpoints, const uint32 checkpoint_id, submatrix_type submatrix, const uint32 submatrix_width, const uint32 submatrix_height, uint8 &state, uint2 &sink, backtracer_type &backtracer)
 
template<uint32 BLOCKDIM, AlignmentType TYPE, typename pattern_string , typename qual_string , typename text_string , typename column_type >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE int32 
alignment_score (const EditDistanceAligner< TYPE > aligner, const pattern_string pattern, const qual_string quals, const text_string text, const int32 min_score, uint2 *sink, column_type column)
 
template<uint32 BAND_LEN, AlignmentType TYPE, typename scoring_type , typename pattern_type , typename qual_type , typename text_type , typename sink_type >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE bool 
banded_alignment_score (const GotohAligner< TYPE, scoring_type > &aligner, pattern_type pattern, qual_type quals, text_type text, const int32 min_score, sink_type &sink)
 
template<uint32 BAND_LEN, AlignmentType TYPE, typename scoring_type , typename pattern_type , typename qual_type , typename text_type , typename sink_type , typename checkpoint_type >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE bool 
banded_alignment_score (const GotohAligner< TYPE, scoring_type > &aligner, pattern_type pattern, qual_type quals, text_type text, const int32 min_score, const uint32 window_begin, const uint32 window_end, sink_type &sink, checkpoint_type checkpoint)
 
template<uint32 BAND_LEN, uint32 CHECKPOINTS, AlignmentType TYPE, typename scoring_type , typename pattern_type , typename qual_type , typename text_type , typename sink_type , typename checkpoint_type >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE bool 
banded_alignment_checkpoints (const GotohAligner< TYPE, scoring_type > &aligner, pattern_type pattern, qual_type quals, text_type text, const int32 min_score, sink_type &sink, checkpoint_type checkpoints)
 
template<uint32 BAND_LEN, uint32 CHECKPOINTS, AlignmentType TYPE, typename scoring_type , typename pattern_string , typename qual_string , typename text_string , typename checkpoint_type , typename submatrix_type >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE uint32 
banded_alignment_submatrix (const GotohAligner< TYPE, scoring_type > &aligner, pattern_string pattern, qual_string quals, text_string text, const int32 min_score, checkpoint_type checkpoints, const uint32 checkpoint_id, submatrix_type submatrix)
 
template<uint32 BAND_LEN, uint32 CHECKPOINTS, AlignmentType TYPE, typename scoring_type , typename checkpoint_type , typename submatrix_type , typename backtracer_type >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE bool 
banded_alignment_traceback (const GotohAligner< TYPE, scoring_type > &aligner, checkpoint_type checkpoints, const uint32 checkpoint_id, submatrix_type submatrix, const uint32 submatrix_height, uint8 &state, uint2 &sink, backtracer_type &backtracer)
 
template<uint32 CHECKPOINTS, AlignmentType TYPE, typename scoring_type , typename checkpoint_type , typename submatrix_type , typename backtracer_type >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE bool 
alignment_traceback (const GotohAligner< TYPE, scoring_type > aligner, checkpoint_type checkpoints, const uint32 checkpoint_id, submatrix_type submatrix, const uint32 submatrix_width, const uint32 submatrix_height, uint8 &state, uint2 &sink, backtracer_type &backtracer)
 
template<uint32 BLOCKDIM, AlignmentType TYPE, typename scoring_type , typename string_type , typename qual_type , typename ref_type , typename column_type >
NVBIO_FORCEINLINE NVBIO_DEVICE
int32 
gotoh_alignment_score (const scoring_type &scoring, const string_type str, const qual_type quals, const ref_type ref, const int32 min_score, uint2 *sink, column_type temp)
 
template<uint32 BLOCKDIM, AlignmentType TYPE, typename scoring_type , typename pattern_string , typename qual_string , typename text_string , typename column_type >
NVBIO_FORCEINLINE NVBIO_DEVICE
int32 
alignment_score (const GotohAligner< TYPE, scoring_type > aligner, const pattern_string pattern, const qual_string quals, const text_string text, const int32 min_score, uint2 *sink, column_type column)
 
template<uint32 CHECKPOINTS, AlignmentType TYPE, typename scoring_type , typename checkpoint_type , typename submatrix_type , typename output_type >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE bool 
alignment_traceback (const HammingDistanceAligner< TYPE, scoring_type > aligner, checkpoint_type checkpoints, const uint32 checkpoint_id, submatrix_type submatrix, const uint32 submatrix_width, const uint32 submatrix_height, uint8 &state, uint2 &sink, output_type &output)
 
template<uint32 BAND_WIDTH>
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE int 
diagonal_column (const uint32 B_c_ref, uint32 &VP, uint32 &VN)
 
template<uint32 BAND_WIDTH>
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE int 
horizontal_column (const uint32 B_c_ref, uint32 &VP, uint32 &VN, const int s)
 
template<uint32 BAND_WIDTH, uint32 C, AlignmentType TYPE, uint32 ALPHABET_SIZE, typename pattern_string , typename text_string , typename sink_type >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE bool 
banded_myers (const pattern_string pattern, const text_string text, const int16 min_score, sink_type &sink)
 
template<uint32 BAND_LEN, AlignmentType TYPE, uint32 ALPHABET_SIZE, typename pattern_type , typename qual_type , typename text_type , typename sink_type >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE bool 
banded_alignment_score (const EditDistanceAligner< TYPE, MyersTag< ALPHABET_SIZE > > &aligner, pattern_type pattern, qual_type quals, text_type text, const int32 min_score, sink_type &sink)
 
template<uint32 BAND_LEN, AlignmentType TYPE, uint32 ALPHABET_SIZE, typename pattern_type , typename qual_type , typename text_type , typename sink_type , typename checkpoint_type >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE bool 
banded_alignment_score (const EditDistanceAligner< TYPE, MyersTag< ALPHABET_SIZE > > &aligner, pattern_type pattern, qual_type quals, text_type text, const int32 min_score, const uint32 window_begin, const uint32 window_end, sink_type &sink, checkpoint_type checkpoint)
 
template<uint32 BAND_LEN, AlignmentType TYPE, typename scoring_type , typename pattern_type , typename qual_type , typename text_type , typename sink_type >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE bool 
banded_alignment_score (const SmithWatermanAligner< TYPE, scoring_type > &aligner, pattern_type pattern, qual_type quals, text_type text, const int32 min_score, sink_type &sink)
 
template<uint32 BAND_LEN, AlignmentType TYPE, typename scoring_type , typename pattern_type , typename qual_type , typename text_type , typename sink_type , typename checkpoint_type >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE bool 
banded_alignment_score (const SmithWatermanAligner< TYPE, scoring_type > &aligner, pattern_type pattern, qual_type quals, text_type text, const int32 min_score, const uint32 window_begin, const uint32 window_end, sink_type &sink, checkpoint_type checkpoint)
 
template<uint32 BAND_LEN, uint32 CHECKPOINTS, AlignmentType TYPE, typename scoring_type , typename pattern_type , typename qual_type , typename text_type , typename sink_type , typename checkpoint_type >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE bool 
banded_alignment_checkpoints (const SmithWatermanAligner< TYPE, scoring_type > &aligner, pattern_type pattern, qual_type quals, text_type text, const int32 min_score, sink_type &sink, checkpoint_type checkpoints)
 
template<uint32 BAND_LEN, uint32 CHECKPOINTS, AlignmentType TYPE, typename scoring_type , typename pattern_string , typename qual_string , typename text_string , typename checkpoint_type , typename submatrix_type >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE uint32 
banded_alignment_submatrix (const SmithWatermanAligner< TYPE, scoring_type > &aligner, pattern_string pattern, qual_string quals, text_string text, const int32 min_score, checkpoint_type checkpoints, const uint32 checkpoint_id, submatrix_type submatrix)
 
template<uint32 BAND_LEN, uint32 CHECKPOINTS, AlignmentType TYPE, typename scoring_type , typename checkpoint_type , typename submatrix_type , typename backtracer_type >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE bool 
banded_alignment_traceback (const SmithWatermanAligner< TYPE, scoring_type > &aligner, checkpoint_type checkpoints, const uint32 checkpoint_id, submatrix_type submatrix, const uint32 submatrix_height, uint8 &state, uint2 &sink, backtracer_type &backtracer)
 
template<uint32 CHECKPOINTS, AlignmentType TYPE, typename scoring_type , typename checkpoint_type , typename submatrix_type , typename output_type >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE bool 
alignment_traceback (const SmithWatermanAligner< TYPE, scoring_type > aligner, checkpoint_type checkpoints, const uint32 checkpoint_id, submatrix_type submatrix, const uint32 submatrix_width, const uint32 submatrix_height, uint8 &state, uint2 &sink, output_type &output)
 
template<uint32 BLOCKDIM, AlignmentType TYPE, typename scoring_type , typename string_type , typename qual_type , typename ref_type , typename column_type >
NVBIO_FORCEINLINE NVBIO_DEVICE
int32 
sw_alignment_score (const scoring_type &scoring, string_type str, qual_type quals, ref_type ref, const int32 min_score, uint2 *sink, column_type temp)
 
template<uint32 BLOCKDIM, AlignmentType TYPE, typename scoring_type , typename pattern_string , typename qual_string , typename text_string , typename column_type >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE int32 
alignment_score (const SmithWatermanAligner< TYPE, scoring_type > aligner, const pattern_string pattern, const qual_string quals, const text_string text, const int32 min_score, uint2 *sink, column_type column)
 

Function Documentation

template<uint32 BLOCKDIM, AlignmentType TYPE, typename pattern_string , typename qual_string , typename text_string , typename column_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 nvbio::aln::priv::alignment_score ( const EditDistanceAligner< TYPE aligner,
const pattern_string  pattern,
const qual_string  quals,
const text_string  text,
const int32  min_score,
uint2 *  sink,
column_type  column 
)

Definition at line 47 of file ed_warp_inl.h.

template<uint32 BLOCKDIM, AlignmentType TYPE, typename scoring_type , typename pattern_string , typename qual_string , typename text_string , typename column_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 nvbio::aln::priv::alignment_score ( const SmithWatermanAligner< TYPE, scoring_type >  aligner,
const pattern_string  pattern,
const qual_string  quals,
const text_string  text,
const int32  min_score,
uint2 *  sink,
column_type  column 
)

Definition at line 218 of file sw_warp_inl.h.

template<uint32 BLOCKDIM, AlignmentType TYPE, typename scoring_type , typename pattern_string , typename qual_string , typename text_string , typename column_type >
NVBIO_FORCEINLINE NVBIO_DEVICE int32 nvbio::aln::priv::alignment_score ( const GotohAligner< TYPE, scoring_type >  aligner,
const pattern_string  pattern,
const qual_string  quals,
const text_string  text,
const int32  min_score,
uint2 *  sink,
column_type  column 
)

Definition at line 264 of file gotoh_warp_inl.h.

template<uint32 CHECKPOINTS, AlignmentType TYPE, typename scoring_type , typename checkpoint_type , typename submatrix_type , typename backtracer_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::aln::priv::alignment_traceback ( const GotohAligner< TYPE, scoring_type >  aligner,
checkpoint_type  checkpoints,
const uint32  checkpoint_id,
submatrix_type  submatrix,
const uint32  submatrix_width,
const uint32  submatrix_height,
uint8 &  state,
uint2 &  sink,
backtracer_type &  backtracer 
)

Definition at line 1806 of file gotoh_inl.h.

template<uint32 BLOCKDIM, AlignmentType TYPE, typename scoring_type , typename string_type , typename qual_type , typename ref_type , typename column_type >
NVBIO_FORCEINLINE NVBIO_DEVICE int32 nvbio::aln::priv::gotoh_alignment_score ( const scoring_type &  scoring,
const string_type  str,
const qual_type  quals,
const ref_type  ref,
const int32  min_score,
uint2 *  sink,
column_type  temp 
)

Definition at line 51 of file gotoh_warp_inl.h.

template<uint32 BLOCKDIM, AlignmentType TYPE, typename scoring_type , typename string_type , typename qual_type , typename ref_type , typename column_type >
NVBIO_FORCEINLINE NVBIO_DEVICE int32 nvbio::aln::priv::sw_alignment_score ( const scoring_type &  scoring,
string_type  str,
qual_type  quals,
ref_type  ref,
const int32  min_score,
uint2 *  sink,
column_type  temp 
)

Definition at line 53 of file sw_warp_inl.h.