Align::Fixed Namespace Reference

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

Functions
void	AlignStatic (const char_t(&querys)[MAX_QUERY_LENGTH], const char_t(&references)[MAX_REFERENCE_LENGTH], const idx_t query_length, const idx_t reference_length, const Penalties &penalties, idx_t &tb_i, idx_t &tb_j, tbr_t(&tb_out)[MAX_REFERENCE_LENGTH+MAX_QUERY_LENGTH])
	Perform Pairwise alignment for two sequences, in fixed banding with virtual coordinates. More...
void	ChunkCompute (const idx_t chunk_row_offset, const input_char_block_t &query, const char_t(&reference)[MAX_REFERENCE_LENGTH], const chunk_col_scores_inf_t &init_col_scr, score_vec_t(&init_row_scr)[MAX_REFERENCE_LENGTH], idx_t p_cols, const idx_t ck_idx, idx_t &l_lim_reg, idx_t &u_lim_reg, const bool(&col_pred)[PE_NUM], const idx_t global_query_length, const idx_t local_query_length, const idx_t reference_length, const Penalties &penalties, ScorePack(&max)[PE_NUM], tbp_t(&chunk_tbp_out)[PE_NUM][TBMEM_SIZE])
	Compute the traceback pointers for a chunk of the size PE_NUM * REFERENCE_LENGTH, with fixed banding and virtual coordinates. More...
void	MapPredicate (const idx_t(&local_l_lim)[PE_NUM], const idx_t(&local_u_lim)[PE_NUM], const idx_t(&virtual_cols)[PE_NUM], const bool(&col_pred)[PE_NUM], bool(&predicate)[PE_NUM])
	Logics to map the global coordinates of a wavefront of PE to their prediate values. MapPredicateSquare is a function F: (pe_row: int, pe_col: int) -> (predicate_balue: boolean) It's unrolled for PE_NUM applying to each PE. More...
template<int PE_NUM_, int MAX_QUERY_LENGTH_>
void	PrepareLocals (const char_t(&query)[MAX_QUERY_LENGTH_], const score_vec_t(&init_col_scr)[MAX_QUERY_LENGTH_], char_t(&local_query)[PE_NUM_], chunk_col_scores_inf_t &init_col_scr_local, bool(&col_pred)[PE_NUM_], const idx_t local_query_len, const idx_t idx)

Detailed Description

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

Function Documentation

void Align::Fixed::AlignStatic	(	const char_t(&)	querys[MAX_QUERY_LENGTH],
		const char_t(&)	references[MAX_REFERENCE_LENGTH],
		const idx_t	query_length,
		const idx_t	reference_length,
		const Penalties &	penalties,
		idx_t &	tb_i,
		idx_t &	tb_j,
		tbr_t(&)	tb_out[MAX_REFERENCE_LENGTH+MAX_QUERY_LENGTH]
	)

Perform Pairwise alignment for two sequences, in fixed banding with virtual coordinates.

Parameters

query,:	Query sequence buffer.
reference,:	Reference sequence buffer.
query_length,:	Length of the query.
reference_length,:	Length of the reference.
tb_streams,:	Output traceback path.

void Align::Fixed::ChunkCompute	(	const idx_t	chunk_row_offset,
		const input_char_block_t &	query,
		const char_t(&)	reference[MAX_REFERENCE_LENGTH],
		const chunk_col_scores_inf_t &	init_col_scr,
		score_vec_t(&)	init_row_scr[MAX_REFERENCE_LENGTH],
		idx_t	p_cols,
		const idx_t	ck_idx,
		idx_t &	l_lim_reg,
		idx_t &	u_lim_reg,
		const bool(&)	col_pred[PE_NUM],
		const idx_t	global_query_length,
		const idx_t	local_query_length,
		const idx_t	reference_length,
		const Penalties &	penalties,
		ScorePack(&)	max[PE_NUM],
		tbp_t(&)	chunk_tbp_out[PE_NUM][TBMEM_SIZE]
	)

Compute the traceback pointers for a chunk of the size PE_NUM * REFERENCE_LENGTH, with fixed banding and virtual coordinates.

Parameters

chunk_row_offset	: The row offset in the whole traceback matrix the beginning of the chunk.
query	: Query sequence with length PE_NUM.
init_col_scr	: Initial score for the first column of this chunk.
query_length	: Length of the query < PE_NUM.
reference_length	: Length of the reference < MAX_REFERENCE_LENGTH.
max	: Score pack of the maximium score of this chunk.

void Align::Fixed::MapPredicate	(	const idx_t(&)	local_l_lim[PE_NUM],
		const idx_t(&)	local_u_lim[PE_NUM],
		const idx_t(&)	virtual_cols[PE_NUM],
		const bool(&)	col_pred[PE_NUM],
		bool(&)	predicate[PE_NUM]
	)

Logics to map the global coordinates of a wavefront of PE to their prediate values. MapPredicateSquare is a function F: (pe_row: int, pe_col: int) -> (predicate_balue: boolean) It's unrolled for PE_NUM applying to each PE.

Parameters

ics	Global Row Coordinates of a Wavefront of PE.
jcs	Global Column Coordinates of a Wavefront of PE.
ref_len	Actual Reference Length.
predicate	Predicate Array.

template<int PE_NUM_, int MAX_QUERY_LENGTH_>

void Align::Fixed::PrepareLocals	(	const char_t(&)	query[MAX_QUERY_LENGTH_],
		const score_vec_t(&)	init_col_scr[MAX_QUERY_LENGTH_],
		char_t(&)	local_query[PE_NUM_],
		chunk_col_scores_inf_t &	init_col_scr_local,
		bool(&)	col_pred[PE_NUM_],
		const idx_t	local_query_len,
		const idx_t	idx
	)