mapping.h File Reference

#include <nvBowtie/bowtie2/cuda/defs.h>
#include <nvBowtie/bowtie2/cuda/utils.h>
#include <nvBowtie/bowtie2/cuda/params.h>
#include <nvBowtie/bowtie2/cuda/seed_hit.h>
#include <nvBowtie/bowtie2/cuda/seed_hit_deque_array.h>
#include <nvBowtie/bowtie2/cuda/reads_def.h>
#include <nvBowtie/bowtie2/cuda/fmindex_def.h>
#include <nvbio/io/utils.h>
#include <nvbio/basic/cuda/pingpong_queues.h>
#include <nvbio/basic/cached_iterator.h>
#include <nvbio/basic/packedstream.h>
#include <nvbio/basic/priority_deque.h>
#include <nvbio/basic/strided_iterator.h>
#include <nvbio/basic/algorithms.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	nvbio::bowtie2::cuda::gather_ranges (const uint32 count, const uint32 n_reads, SeedHitDequeArrayDeviceView hits, const uint32 *hit_counts_scan, uint64 *out_ranges)
void	nvbio::bowtie2::cuda::map_whole_read (const ReadsDef::type &read_batch, const FMIndexDef::type fmi, const FMIndexDef::type rfmi, const nvbio::cuda::PingPongQueuesView< uint32 > queues, uint8 *reseed, SeedHitDequeArrayDeviceView hits, const ParamsPOD params, const bool fw, const bool rc)
void	nvbio::bowtie2::cuda::map_exact (const ReadsDef::type &read_batch, const FMIndexDef::type fmi, const FMIndexDef::type rfmi, const uint32 retry, const nvbio::cuda::PingPongQueuesView< uint32 > queues, uint8 *reseed, SeedHitDequeArrayDeviceView hits, const ParamsPOD params, const bool fw, const bool rc)
void	nvbio::bowtie2::cuda::map_exact (const ReadsDef::type &read_batch, const FMIndexDef::type fmi, const FMIndexDef::type rfmi, SeedHitDequeArrayDeviceView hits, const uint2 seed_range, const ParamsPOD params, const bool fw, const bool rc)
void	nvbio::bowtie2::cuda::map_approx (const ReadsDef::type &read_batch, const FMIndexDef::type fmi, const FMIndexDef::type rfmi, const uint32 retry, const nvbio::cuda::PingPongQueuesView< uint32 > queues, uint8 *reseed, SeedHitDequeArrayDeviceView hits, const ParamsPOD params, const bool fw, const bool rc)
void	nvbio::bowtie2::cuda::map_approx (const ReadsDef::type &read_batch, const FMIndexDef::type fmi, const FMIndexDef::type rfmi, SeedHitDequeArrayDeviceView hits, const uint2 seed_range, const ParamsPOD params, const bool fw, const bool rc)
void	nvbio::bowtie2::cuda::map (const ReadsDef::type &read_batch, const FMIndexDef::type fmi, const FMIndexDef::type rfmi, const uint32 retry, const nvbio::cuda::PingPongQueuesView< uint32 > queues, uint8 *reseed, SeedHitDequeArrayDeviceView hits, const ParamsPOD params, const bool fw, const bool rc)