Namespace including the functions of the kernel architecture. More...

Namespaces
	FindMax
	Namespace related to functions used to find the maximum elements in in the score matrix.

	Fixed
	This namespace contains functions to define the core architectures used in the fixed banding alignment kernel.

	Rectangular
	This namespace contains functions to define the core architectures used in the non-banding alignment kernel.

Functions
void	PrepareLocalQuery (char_t(&query)[MAX_QUERY_LENGTH], char_t(&local_query)[PE_NUM], const idx_t offset)
	At beginning of the computation of each strip, it copy a PE_NUM number of the global query characters into the local query buffer. More...

void	InitializeChunkColScore (score_vec_t(&init_col_scr)[PE_NUM], stream_of_blocks< dp_mem_block_t > &dp_mem_out)

void	PrepareScoresArr (dp_mem_block_t &dp_mem_in, score_vec_t(&init_col_scr)[PE_NUM], int id, score_vec_t(&last_chunk_scr)[2], wavefront_scores_t &up_out, wavefront_scores_t &diag_out, wavefront_scores_t &left_out)

template<int PE_NUM_T>
void	PrepareLocals (const char_t(&query)[MAX_QUERY_LENGTH], char_t(&local_query)[PE_NUM_T], score_vec_t(&init_col_scr)[MAX_QUERY_LENGTH], chunk_col_scores_inf_t &init_col_scr_local, bool(&col_pred)[PE_NUM], const idx_t local_query_len, const idx_t idx)
	This function merge PrepareLocalQuery function and CopyColScore function into one, where CopyColScore is a function to copy a column of initial scores from the global buffer to each PE's local buffer before the computation of each chunk. More...

void	InitializeChunkCoordinates (idx_t chunk_row_offset, idx_t chunk_col_offset, hls::vector< idx_t, PE_NUM > &ic, hls::vector< idx_t, PE_NUM > &jc)
	Initialize two lists of coordinates, x coordinate and y coordinate, for each chunk. Theis function is called within the chunk compute function. This is especially useful if the chunk doesn't start at the beginning, i.e. after chunk column offset is developed. More...

void	ArrangeTBP (const tbp_vec_t &tbp_in, const idx_t &p_col_offset, const bool(&predicate)[PE_NUM], tbp_t(&chunk_tbp_out)[PE_NUM][TBMEM_SIZE])

void	ShiftPredicate (bool(&predicate)[PE_NUM], int idx, int query_len, int reference_len)
	Determine the predicate values by constantantly shifting the predicate array with truth values. More...

void	ShiftReference (char_t(&local_reference)[PE_NUM], const char_t(&reference)[MAX_REFERENCE_LENGTH], int idx, int ref_len)
	Shift into the local reference buffer a new reference element, given current wavefront index and reference length. More...

void	PreserveRowScore (score_vec_t(&preserved_row_scr)[MAX_REFERENCE_LENGTH], const score_vec_t score_vec, const bool predicate_pe_last, const idx_t idx)
	Write the last PE's output score to the preserved_row_score buffer to be used in the next chunk. More...

void	UpdateDPMem (dp_mem_block_t &dp_mem, idx_t i, chunk_col_scores_inf_t &init_col_scr, score_vec_t(&init_row_scr)[MAX_REFERENCE_LENGTH])
	Updated the content of the DP Memory with the new scores. It saparates the step of shifting and setting the specific cell with initial scores. More...

void	UpdateDPMemShift (dp_mem_block_t &dp_mem)

void	UpdateDPMemSet (dp_mem_block_t &dp_mem, idx_t i, chunk_col_scores_inf_t &init_col_scr, score_vec_t(&init_row_scr)[MAX_REFERENCE_LENGTH])

void	InitializeScores (score_vec_t(&init_col_scr)[MAX_QUERY_LENGTH], score_vec_t(&init_row_scr)[MAX_REFERENCE_LENGTH], const Penalties &penalties)
	Initialize initial scores for the first column and row on the device. More...

void	ChunkMax (ScorePack &max, ScorePack new_scr)

void	UpdatePEOffset (idx_t(&pe_offset)[PE_NUM], bool(&predicate)[PE_NUM])

void	CopyColScore (chunk_col_scores_inf_t &init_col_scr_local, score_vec_t(&init_col_scr)[MAX_QUERY_LENGTH], idx_t i)

void	UpdateDPMemSep (score_vec_t(&dp_mem)[PE_NUM+1][2], score_vec_t(&score_in)[PE_NUM+1])

void	PrepareScoreBuffer (score_vec_t(&score_buff)[PE_NUM+1], const idx_t i, const chunk_col_scores_inf_t(&init_col_scr), const score_vec_t(&init_row_scr)[MAX_REFERENCE_LENGTH])

Detailed Description

Namespace including the functions of the kernel architecture.

Function Documentation

void Align::ArrangeTBP	(	const tbp_vec_t &	tbp_in,
		const idx_t &	p_col_offset,
		const bool(&)	predicate[PE_NUM],
		tbp_t(&)	chunk_tbp_out[PE_NUM][TBMEM_SIZE]
	)

Store the traceback pointers of PE at the correct location in the traceback pointer matrix, based on the predicate and current p_col_offset.

Parameters

tbp_in	The buffer receiving the traceback pointer from the PE output.
p_col_offset	Physical column of a wavefront of traceback pointers.
predicate	Predicates.
chunk_tbp_out	The traceback pointer memory.

void Align::ChunkMax	(	ScorePack &	max,
		ScorePack	new_scr
	)

void Align::CopyColScore	(	chunk_col_scores_inf_t &	init_col_scr_local,
		score_vec_t(&)	init_col_scr[MAX_QUERY_LENGTH],
		idx_t	i
	)

void Align::InitializeChunkColScore	(	score_vec_t(&)	init_col_scr[PE_NUM],
		stream_of_blocks< dp_mem_block_t > &	dp_mem_out
	)

void Align::InitializeChunkCoordinates	(	idx_t	chunk_row_offset,
		idx_t	chunk_col_offset,
		hls::vector< idx_t, PE_NUM > &	ic,
		hls::vector< idx_t, PE_NUM > &	jc
	)

Initialize two lists of coordinates, x coordinate and y coordinate, for each chunk. Theis function is called within the chunk compute function. This is especially useful if the chunk doesn't start at the beginning, i.e. after chunk column offset is developed.

Parameters

chunk_row_offset	Initial Row of a Chunk
chunk_col_offset	Initial Column of a Chunk.
ic	Actual Global Coordinates for i.
jc	Actual Global Coordinates for j.

void Align::InitializeScores	(	score_vec_t(&)	init_col_scr[MAX_QUERY_LENGTH],
		score_vec_t(&)	init_row_scr[MAX_REFERENCE_LENGTH],
		const Penalties &	penalties
	)

Initialize initial scores for the first column and row on the device.

Parameters

init_col_scr,:	Initial scores for the first column.
init_row_scr,:	Initial scores for the first row.

void Align::PrepareLocalQuery	(	char_t(&)	query[MAX_QUERY_LENGTH],
		char_t(&)	local_query[PE_NUM],
		const idx_t	offset
	)

At beginning of the computation of each strip, it copy a PE_NUM number of the global query characters into the local query buffer.

Parameters

query	Query sequence
local_query	Local query is a buffer of PE_NUM length that is read in parallel by PEs during the wavefront computation.
offset	The offset in the global query to start copying.

template<int PE_NUM_T>

void Align::PrepareLocals	(	const char_t(&)	query[MAX_QUERY_LENGTH],
		char_t(&)	local_query[PE_NUM_T],
		score_vec_t(&)	init_col_scr[MAX_QUERY_LENGTH],
		chunk_col_scores_inf_t &	init_col_scr_local,
		bool(&)	col_pred[PE_NUM],
		const idx_t	local_query_len,
		const idx_t	idx
	)

This function merge PrepareLocalQuery function and CopyColScore function into one, where CopyColScore is a function to copy a column of initial scores from the global buffer to each PE's local buffer before the computation of each chunk.

Template Parameters

PE_NUM_T Number of PE

Parameters

query	Query Sequence
local_query	Local Query Buffer
init_col_scr	Initial Column Scores
init_col_scr_local	Local Initial Column Score Buffer.
idx	The offset in the global buffer to copy.

void Align::PrepareScoreBuffer	(	score_vec_t(&)	score_buff[PE_NUM+1],
		const idx_t	i,
		const chunk_col_scores_inf_t &	init_col_scr,
		const score_vec_t(&)	init_row_scr[MAX_REFERENCE_LENGTH]
	)

void Align::PrepareScoresArr	(	dp_mem_block_t &	dp_mem_in,
		score_vec_t(&)	init_col_scr[PE_NUM],
		int	id,
		score_vec_t(&)	last_chunk_scr[2],
		wavefront_scores_t &	up_out,
		wavefront_scores_t &	diag_out,
		wavefront_scores_t &	left_out
	)

void Align::PreserveRowScore	(	score_vec_t(&)	preserved_row_scr[MAX_REFERENCE_LENGTH],
		const score_vec_t	score_vec,
		const bool	predicate_pe_last,
		const idx_t	idx
	)

Write the last PE's output score to the preserved_row_score buffer to be used in the next chunk.

Parameters

score_vec	The last PE's output score.
predicate_pe_last	The last PE's predicate value. Write out the score only if the predicate is true.
idx	The index in the buffer to write.

void Align::ShiftPredicate	(	bool(&)	predicate[PE_NUM],
		int	idx,
		int	query_len,
		int	reference_len
	)

Determine the predicate values by constantantly shifting the predicate array with truth values.

Parameters

predicate	Predicate Array.
idx	Wavefront Index.
query_len	Actual query Length.
reference_len	Actual reference Length.

void Align::ShiftReference	(	char_t(&)	local_reference[PE_NUM],
		const char_t(&)	reference[MAX_REFERENCE_LENGTH],
		int	idx,
		int	ref_len
	)

Shift into the local reference buffer a new reference element, given current wavefront index and reference length.

Parameters

local_reference	The local reference buffer.
reference	The reference.
idx	Wavefront index.
ref_len	Actual reference length.

void Align::UpdateDPMem	(	dp_mem_block_t &	dp_mem,
		idx_t	i,
		chunk_col_scores_inf_t &	init_col_scr,
		score_vec_t(&)	init_row_scr[MAX_REFERENCE_LENGTH]
	)

Updated the content of the DP Memory with the new scores. It saparates the step of shifting and setting the specific cell with initial scores.

Deprecated:: This function is deprecated. Please see UpdateDPMemSep which is used in the kernel. .

Parameters

dp_mem	DP Memory
i	The index of the wavefront.
init_col_scr	Initial Column Scores
init_row_scr	Initial Row Scores

void Align::UpdateDPMemSep	(	score_vec_t(&)	dp_mem[PE_NUM+1][2],
		score_vec_t(&)	score_in[PE_NUM+1]
	)

void Align::UpdateDPMemSet	(	dp_mem_block_t &	dp_mem,
		idx_t	i,
		chunk_col_scores_inf_t &	init_col_scr,
		score_vec_t(&)	init_row_scr[MAX_REFERENCE_LENGTH]
	)

void Align::UpdateDPMemShift ( dp_mem_block_t & dp_mem )

void Align::UpdatePEOffset	(	idx_t(&)	pe_offset[PE_NUM],
		bool(&)	predicate[PE_NUM]
	)

Namespaces

Functions

Detailed Description

Function Documentation