xtn.cu File Reference

The core algorithm on a low-level abstraction concerning how buffers, streamings, and memory management techniques fit together. More...

#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "xtn_overlap_inner.cu"

Functions
MemoryContext	initMemory (int seqLen, bool isGPU)
	private function. More...
int	cal_max_exponent (size_t input)
	private function. More...
MemoryContext	cal_memory_stream1 (int seqLen, int distance)
	calculate memory constraint for stream 1 using the upper bound of the memory allocation during the operation. More...
MemoryContext	cal_memory_stream2 (int seqLen)
	calculate memory constraint for stream 2 using the upper bound of the memory allocation during the operation. More...
MemoryContext	cal_memory_stream3 (int seqLen)
	calculate memory constraint for stream 3 using the upper bound of the memory allocation during the operation. More...
MemoryContext	cal_memory_stream4 (int seqLen, bool overlapMode)
	calculate memory constraint for stream 4 using the upper bound of the memory allocattion during the operation. More...
MemoryContext	cal_memory_lowerbound (int seqLen)
	calculate RAM constraint for lower bound calculation. More...
void	write_b3 (Int2 *pairOutput, int pairLen)
	callback function to write generated pairs. More...
int *	concat_histograms (std::vector< int *> histograms, MemoryContext ctx)
	flatten histograms stored as vector<int*> to a 1D array. More...
int	cal_lowerbounds (std::vector< int *> histograms, int *&lowerbounds, int seqLen, int *buffer)
	calculate the lowerbounds from the collected histogram and memory constraints. More...
template<typename T1 , typename T2 >
int **	set_d2_offsets (std::vector< int *> histograms, D2Stream< T1 > *s1, D2Stream< T2 > *s2, int *buffer, MemoryContext ctx)
	apply precalculated bin packing offset to the given 2D buffers. More...
void	xtn_perform (XTNArgs args, SeqArray *seqArr, SeqInfo *seqInfo, void callback(XTNOutput))
	the main function for XT-neighbor algorithm. More...

Variables
D2Stream< Int2 > *	b3 = NULL
const int	MAX_PROCESSING = 1 << 30

Detailed Description

The core algorithm on a low-level abstraction concerning how buffers, streamings, and memory management techniques fit together.

Function Documentation

cal_lowerbounds()

int cal_lowerbounds	(	std::vector< int *>	histograms,
		int *&	lowerbounds,
		int	seqLen,
		int *	buffer
	)

calculate the lowerbounds from the collected histogram and memory constraints.

cal_max_exponent()

int cal_max_exponent

(

size_t

input

)

private function.

cal_memory_lowerbound()

MemoryContext cal_memory_lowerbound

(

int

seqLen

)

calculate RAM constraint for lower bound calculation.

cal_memory_stream1()

MemoryContext cal_memory_stream1	(	int	seqLen,
		int	distance
	)

calculate memory constraint for stream 1 using the upper bound of the memory allocation during the operation.

cal_memory_stream2()

MemoryContext cal_memory_stream2

(

int

seqLen

)

calculate memory constraint for stream 2 using the upper bound of the memory allocation during the operation.

cal_memory_stream3()

MemoryContext cal_memory_stream3

(

int

seqLen

)

calculate memory constraint for stream 3 using the upper bound of the memory allocation during the operation.

cal_memory_stream4()

MemoryContext cal_memory_stream4	(	int	seqLen,
		bool	overlapMode
	)

calculate memory constraint for stream 4 using the upper bound of the memory allocattion during the operation.

concat_histograms()

int* concat_histograms	(	std::vector< int *>	histograms,
		MemoryContext	ctx
	)

flatten histograms stored as vector<int*> to a 1D array.

initMemory()

MemoryContext initMemory	(	int	seqLen,
		bool	isGPU
	)

private function.

set_d2_offsets()

template<typename T1 , typename T2 >

int** set_d2_offsets	(	std::vector< int *>	histograms,
		D2Stream< T1 > *	s1,
		D2Stream< T2 > *	s2,
		int *	buffer,
		MemoryContext	ctx
	)

apply precalculated bin packing offset to the given 2D buffers.

write_b3()

void write_b3	(	Int2 *	pairOutput,
		int	pairLen
	)

callback function to write generated pairs.

xtn_perform()

void xtn_perform	(	XTNArgs	args,
		SeqArray *	seqArr,
		SeqInfo *	seqInfo,
		void	callbackXTNOutput
	)

the main function for XT-neighbor algorithm.

Parameters

args	all flags parsed from command line
seqArr	sequence input
seqInfo	information of each CDR3 sequence, only used in overlap mode
callback	function to be invoked once a chunk of output is ready

Variable Documentation

b3

D2Stream<Int2>* b3 = NULL

MAX_PROCESSING

const int MAX_PROCESSING = 1 << 30