Detailed Description

Algorithm tags are used to specify a DP algorithm. In order to avoid expensive memory transactions, the algorithms we designed block the matrix in stripes that are processed in registers. The blocking can happen either along the pattern or along the text. To communicate the values across stripes, the right-most column of each stripe must be stored in memory - hence the two algorithms differ for the amount of temporary storage needed (for long texts, text-blocking is preferred).

: Additionally, for edit distance, the Myers bit-vector algorithm is available.

Classes
struct	nvbio::aln::PatternBlockingTag
	block along the pattern More...

struct	nvbio::aln::TextBlockingTag
	block along the text (at the moment, this is only supported for scoring) More...

struct	nvbio::aln::MyersTag< ALPHABET_SIZE_T >
	Myers bit-vector algorithm. More...

struct	nvbio::aln::transpose_tag< T >

struct	nvbio::aln::transpose_tag< PatternBlockingTag >

struct	nvbio::aln::transpose_tag< TextBlockingTag >

struct	nvbio::aln::transpose_aligner< T >

Detailed Description

Classes