ALIGN_TYPE Namespace Reference

This namespace contains the functions that is required to be implemented by the user. ALIGN_TYPE itself is a macro, and is supposed to be defined as the kernel name in params.h. More...

Namespaces
	Helper
	PE
	Traceback
	The namespace for the customized function related to the traceback.

Functions
void	InitializeScores (score_vec_t(&init_col_scr)[MAX_QUERY_LENGTH], score_vec_t(&init_row_scr)[MAX_REFERENCE_LENGTH], Penalties penalties)
	The function to initialize the initial row and column scores. More...
void	UpdatePEMaximum (const wavefront_scores_inf_t scores, ScorePack(&max)[PE_NUM], const idx_t chunk_row_offset, const idx_t wavefront, const idx_t p_cols, const idx_t ck_idx, const bool(&predicate)[PE_NUM], const idx_t query_len, const idx_t ref_len)
	This function unrolls PE_NUM units to compare the their local maximum/minimum and new cell scores. It can be queried to update the local minimum/maximum scores based on it's current index. The row index can be computed as the PE_idx + chunk_row_offset; and the column index is the wavefront index - PE_idx. The actual query and reference lengths are provided so that they can be compared to the current index. More...
void	InitializeMaxScores (ScorePack(&max)[PE_NUM], idx_t qry_len, idx_t ref_len)
	Initialize the ScorePacks with the minimum/maximum values. More...

Detailed Description

This namespace contains the functions that is required to be implemented by the user. ALIGN_TYPE itself is a macro, and is supposed to be defined as the kernel name in params.h.

Declare Any Customized Align type in this file.

Function Documentation

void ALIGN_TYPE::InitializeMaxScores	(	ScorePack(&)	max[PE_NUM],
		idx_t	qry_len,
		idx_t	ref_len
	)

Initialize the ScorePacks with the minimum/maximum values.

A way to save resources in the global alignment is to initialize the PE to start the traceback with a INF value and others NINF. The physical coordinates can be pre-calculated before knowing the scores, thus save the resources by having empty UpdatePEMaximum function. See the DP-HLS global alignment example for the actual implementation.

Parameters

qry_len	Actual query length.
ref_len	Actual reference length.

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

The function to initialize the initial row and column scores.

Parameters

penalties

The penalties (alignment parameters).

void ALIGN_TYPE::UpdatePEMaximum	(	const wavefront_scores_inf_t	scores,
		ScorePack(&)	max[PE_NUM],
		const idx_t	chunk_row_offset,
		const idx_t	wavefront,
		const idx_t	p_cols,
		const idx_t	ck_idx,
		const bool(&)	predicate[PE_NUM],
		const idx_t	query_len,
		const idx_t	ref_len
	)

This function unrolls PE_NUM units to compare the their local maximum/minimum and new cell scores. It can be queried to update the local minimum/maximum scores based on it's current index. The row index can be computed as the PE_idx + chunk_row_offset; and the column index is the wavefront index - PE_idx. The actual query and reference lengths are provided so that they can be compared to the current index.

Parameters

scores	The buffer of output scores.
chunk_row_offset	The row offset of the current chunk.
wavefront	The wavefront index.
p_cols	The physical column corresponding to the output scores.
ck_idx	The chunk index.
query_len	Query length.
ref_len	Reference length.