reconstruct.h File Reference

Reconstruction functions header. More...

#include "chain.h"
#include "scorer.h"
#include "thread.h"

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Functions
void	nwReconstruct (char **path, int *pathLen, int *outScore, Chain *query, int queryFrontGap, int queryBackGap, Chain *target, int targetFrontGap, int targetBackGap, Scorer *scorer, int score, int *cards, int cardsLen, Thread *thread)
	Needleman-Wunsch reconstruction implementation. More...

Detailed Description

Reconstruction functions header.

Function Documentation

void nwReconstruct	(	char **	path,
		int *	pathLen,
		int *	outScore,
		Chain *	query,
		int	queryFrontGap,
		int	queryBackGap,
		Chain *	target,
		int	targetFrontGap,
		int	targetBackGap,
		Scorer *	scorer,
		int	score,
		int *	cards,
		int	cardsLen,
		Thread *	thread
	)

Needleman-Wunsch reconstruction implementation.

If the score is provided function uses Ukkonen's banded optimization. Function also utilizes Hirschberg's algorithm and therefore is linear in memory. QueryFrontGap and targetFrontGap arguments can't both be not equal to 0. QueryBackGap and targetBackGap arguments can't both be not equal to 0. For path format see Alignment. If needed function utilzes provided CUDA cards.

Parameters

path	output path
pathLen	output path length
outScore	output score
query	query chain
queryFrontGap	if not equal to 0, force that path starts in MOVE_UP
queryBackGap	if not equal to 0, force that path ends in MOVE_UP
target	target chain
targetFrontGap	if not equal to 0, force that path starts in MOVE_LEFT
targetBackGap	if not equal to 0, force that path ends in MOVE_LEFT
scorer	scorer object used for alignment
score	input alignment score if known, otherwise NO_SCORE
cards	cuda cards index array
cardsLen	cuda cards index array length
thread	thread on which the function will be executed, if NULL function is executed on the current thread