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.

Namespaces

Classes

Functions

Function Documentation