theplu::yat::utility::SmithWaterman Class Reference

#include <yat/utility/SmithWaterman.h>

Public Member Functions
	SmithWaterman (double gap=0, double open_gap=0)
	Constructor. More...
	SmithWaterman (double vertical_gap, double open_vertical_gap, double horizon_gap, double open_horizon_gap)
	Constructor. More...
const Aligner::Cigar &	cigar (void) const
size_t	position (void) const
const Matrix &	score (void) const
double	operator() (const Matrix &dot)
template<typename RandomAccessIterator1 , typename RandomAccessIterator2 >
double	operator() (RandomAccessIterator1 reference_begin, RandomAccessIterator1 reference_end, RandomAccessIterator2 query_begin, RandomAccessIterator2 query_end, double mismatch=0)

Detailed Description

Since

New in yat 0.12

Constructor & Destructor Documentation

theplu::yat::utility::SmithWaterman::SmithWaterman ( double  gap = 0, double  open_gap = 0  )

explicit

Constructor.

Same as SmithWaterman(gap, open_gap, gap, open_gap)

theplu::yat::utility::SmithWaterman::SmithWaterman	(	double	vertical_gap,
		double	open_vertical_gap,
		double	horizon_gap,
		double	open_horizon_gap
	)

Constructor.

Parameters

vertical_gap	Penalty for extending a vertical gap. A vertical gap means consuming a reference element i.e. a deletion in query sequence.
open_vertical_gap	Open a deletion. Total cost for a deletion is open_vertical_gap + N * vertical_gap.
horizon_gap	Penalty for extending a insertion.
open_horizon_gap	Penalty for open an insertion. Total penalty for a insertion is open_horizon_gap + N * horizon_gap.

Member Function Documentation

const Aligner::Cigar& theplu::yat::utility::SmithWaterman::cigar

(

void

)

const

The CIGAR here is slightly different compared to CIGAR in Aligner as it uses BAM_CEQUAL and BAM_CDIFF rather than BAM_CMATCH, and it also uses BAM_CSOFT_CLIP and ends of CIGAR to reflect if whole query was aligned.

Returns

CIGAR reflecting latest performed alignment

double theplu::yat::utility::SmithWaterman::operator()

(

const Matrix &

dot

)

Find best alignment using Smith-Waterman algorithm based on the dot-matrix. Each row in dot corresponds to an element in reference, and each column corresponds to an element in the query.

Returns

smith-waterman score

template<typename RandomAccessIterator1 , typename RandomAccessIterator2 >

double theplu::yat::utility::SmithWaterman::operator()	(	RandomAccessIterator1	reference_begin,
		RandomAccessIterator1	reference_end,
		RandomAccessIterator2	query_begin,
		RandomAccessIterator2	query_end,
		double	mismatch = 0
	)

Calculate a dot-matrix of size query_end-query_begin X reference_end-reference_begin where the element ij is 1.0 if reference_begin[i] == query_begin[j] and -mismatch otherwise.

Type Requirements:

• RandomAccessIterator1 is a Readable Iterator
• RandomAccessIterator1 is a Random Access Traversal Iterator
• RandomAccessIterator2 is a Readable Iterator
• RandomAccessIterator2 is a Random Access Traversal Iterator

size_t theplu::yat::utility::SmithWaterman::position

(

void

)

const

Returns

position i.e. first element in reference that is aligned to the query.

const Matrix& theplu::yat::utility::SmithWaterman::score

(

void

)

const

Returns

score matrix

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The documentation for this class was generated from the following file:

• yat/utility/SmithWaterman.h