xtn_overlap_inner.cu File Reference

A collection of patching functions that add repertoire-comparison functionality to xtn_overlap.cu. More...

#include "xtn_inner.cu"

Functions
__global__ void	_setGlobalVar (char *allStr, unsigned int *allStrOffset)
	private function More...
int	deduplicate_full_length (char *allStr, unsigned int *allStrOffsets, SeqInfo *&info, Int3 *&seqOut, int *&infoLenOut, int seqLen, int *buffer)
	deduplicate the sequence on the full length level and generate related data More...
int	overlap_mode_init (char *allStr, unsigned int *allStrOffsets, Int3 *&seqOut, SeqInfo *&info, int *&infoOffsetOut, std::vector< XTNOutput > &allOutputs, int seqLen, int *buffer)
	deduplicate input and initialize output variable More...
void	stream_handler4_overlap (Chunk< Int2 > pairInput, std::vector< XTNOutput > &allOutputs, char *allStr, unsigned int *allStrOffsets, SeqInfo *seqInfo, int *seqOffset, int seqLen, int distance, char measure, int *buffer, MemoryContext ctx)
	handle all GPU operations in stream 4 overlap mode. More...
XTNOutput	mergeOutput (std::vector< XTNOutput > allOutputs, int *buffer)
	merge all outputs by grouping the index keys and summing the frequency values. More...

Variables
__device__ char *	_allStr = NULL
	private variable More...
__device__ unsigned int *	_allStrOffset = NULL
	private variable More...

Detailed Description

A collection of patching functions that add repertoire-comparison functionality to xtn_overlap.cu.

Function Documentation

_setGlobalVar()

__global__ void _setGlobalVar	(	char *	allStr,
		unsigned int *	allStrOffset
	)

private function

deduplicate_full_length()

int deduplicate_full_length	(	char *	allStr,
		unsigned int *	allStrOffsets,
		SeqInfo *&	info,
		Int3 *&	seqOut,
		int *&	infoLenOut,
		int	seqLen,
		int *	buffer
	)

deduplicate the sequence on the full length level and generate related data

Parameters

allStr	container of all sequences
allStrOffsets	start/end position of each sequence
info	information of each input sequence, will be sorted as the side-effect of this operation
seqOut	deduplicated sequence in Int3 form
infoLenOut	count of each duplicated sequence, has the same length as seqOut
seqLen	number of input sequence
buffer	integer buffer

Returns

the length of seqOut

mergeOutput()

XTNOutput mergeOutput	(	std::vector< XTNOutput >	allOutputs,
		int *	buffer
	)

merge all outputs by grouping the index keys and summing the frequency values.

Parameters

allOutputs	container of generated results
buffer	integer buffer

Returns

merged results

overlap_mode_init()

int overlap_mode_init	(	char *	allStr,
		unsigned int *	allStrOffsets,
		Int3 *&	seqOut,
		SeqInfo *&	info,
		int *&	infoOffsetOut,
		std::vector< XTNOutput > &	allOutputs,
		int	seqLen,
		int *	buffer
	)

deduplicate input and initialize output variable

Parameters

allStr	container of all sequences
allStrOffsets	start/end position of each sequence
seqOut	return sequence in Int3 form
info	information of each input sequence, will be sorted as the side-effect of this operation
infoOffsetOut	offset of each info for each unique sequence
allOutputs	container of generated result
seqLen	number of input sequence
buffer	integer buffer

Returns

the length of seqOut

stream_handler4_overlap()

void stream_handler4_overlap	(	Chunk< Int2 >	pairInput,
		std::vector< XTNOutput > &	allOutputs,
		char *	allStr,
		unsigned int *	allStrOffsets,
		SeqInfo *	seqInfo,
		int *	seqOffset,
		int	seqLen,
		int	distance,
		char	measure,
		int *	buffer,
		MemoryContext	ctx
	)

handle all GPU operations in stream 4 overlap mode.

Parameters

pairInput	nearest neighbor pairs
allOutputs	container of generated results
allStr	container of all sequences
allStrOffsets	start/end position of each sequence
seqInfo	information of each sequence
seqOffset	offset of seqInfo array
seqLen	number of input CDR3 sequences
distance	distance threshold
measure	type of measurement (levenshtein/hamming)
buffer	integer buffer
ctx	memory context

Variable Documentation

_allStr

__device__ char* _allStr = NULL

private variable

_allStrOffset

__device__ unsigned int* _allStrOffset = NULL

private variable