generate_combination.cu File Reference

A single method which generates all possible deletions of a CDR3 string within a given Levenshtein threshold. More...

#include "codec.cu"

Functions
__device__ void	printStack (int *indexStack, int length)
	private method More...
__device__ void	expand_values (int index, int *output, int start, int end)
	private method More...
__device__ void	expand_keys (Int3 seq, int distance, Int3 *output, unsigned int *firstKeys, int start, int end)
	private method More...
__device__ void	expand_keys_static (Int3 seq, int distance, Int3 *output, unsigned int *firstKeys, int start, int end)
	private method More...
__global__ void	gen_combination (Int3 *seqs, int *combinationOffsets, int distance, Int3 *combinationKeys, int *combinationValues, int carry, unsigned int *firstKeys, int n)
	Generate all combinations of deletion for sequences using expand primitive. More...

Variables
const int	MAX_DISTANCE = 2

Detailed Description

A single method which generates all possible deletions of a CDR3 string within a given Levenshtein threshold.

Function Documentation

expand_keys()

__device__ void expand_keys	(	Int3	seq,
		int	distance,
		Int3 *	output,
		unsigned int *	firstKeys,
		int	start,
		int	end
	)

private method

expand_keys_static()

__device__ void expand_keys_static	(	Int3	seq,
		int	distance,
		Int3 *	output,
		unsigned int *	firstKeys,
		int	start,
		int	end
	)

private method

expand_values()

__device__ void expand_values	(	int	index,
		int *	output,
		int	start,
		int	end
	)

private method

gen_combination()

__global__ void gen_combination	(	Int3 *	seqs,
		int *	combinationOffsets,
		int	distance,
		Int3 *	combinationKeys,
		int *	combinationValues,
		int	carry,
		unsigned int *	firstKeys,
		int	n
	)

Generate all combinations of deletion for sequences using expand primitive.

For a given index, multiple key value pairs are generated with a combination as key and index as value.

This implementation doesn't use recursive for performance reason.

Parameters

seqs	sequence to expand
combinationOffsets	precalculated memory position of the output
distance	Levenshtein distance threshold
combinationKeys	key output
combinationValues	value output
carry	the offset of the current chunk
firstKeys	partial key output for histogram
n	array length of seqs and combinationOffsets

printStack()

__device__ void printStack	(	int *	indexStack,
		int	length
	)

private method

Variable Documentation

MAX_DISTANCE

const int MAX_DISTANCE = 2