nvBowtie.cpp File Reference

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <string>
#include <nvbio/basic/console.h>
#include <nvbio/basic/exceptions.h>
#include <nvbio/basic/shared_pointer.h>
#include <nvbio/io/fmindex/fmindex.h>
#include <nvbio/io/sequence/sequence.h>
#include <nvbio/io/sequence/sequence_mmap.h>
#include <nvbio/io/output/output_file.h>
#include <nvBowtie/bowtie2/cuda/params.h>
#include <nvBowtie/bowtie2/cuda/stats.h>
#include <nvBowtie/bowtie2/cuda/input_thread.h>
#include <nvBowtie/bowtie2/cuda/compute_thread.h>
#include <nvbio/basic/omp.h>

Go to the source code of this file.

Namespaces
	nvbio
	Define a vector_view POD type and plain_view() for std::vector.
	nvbio::bowtie2
	nvbio::bowtie2::cuda

Functions
void	crcInit ()
void	nvbio::bowtie2::cuda::test_seed_hit_deques ()
void	nvbio::bowtie2::cuda::test_scoring_queues ()
bool	is_number (const char *str, uint32 len=uint32(-1))
void	log_ed (nvbio::bowtie2::cuda::AlignmentStats &stats)
void	log_mapq (nvbio::bowtie2::cuda::AlignmentStats &stats)
int	main (int argc, char *argv[])

Function Documentation

void crcInit

(

)

Definition at line 99 of file crc.cpp.

bool is_number	(	const char *	str,
		uint32	len = uint32(-1)
	)

Definition at line 64 of file nvBowtie.cpp.

void log_ed

(

nvbio::bowtie2::cuda::AlignmentStats &

stats)

Definition at line 79 of file nvBowtie.cpp.

void log_mapq

(

nvbio::bowtie2::cuda::AlignmentStats &

stats)

Definition at line 100 of file nvBowtie.cpp.

int main	(	int	argc,
		char *	argv[]
	)

Definition at line 115 of file nvBowtie.cpp.