traceback_impl.h File Reference

#include <nvBowtie/bowtie2/cuda/defs.h>
#include <nvBowtie/bowtie2/cuda/params.h>
#include <nvBowtie/bowtie2/cuda/string_utils.h>
#include <nvBowtie/bowtie2/cuda/scoring.h>
#include <nvbio/alignment/alignment.h>
#include <nvbio/alignment/batched.h>
#include <nvbio/basic/exceptions.h>
#include <nvbio/io/alignments.h>
#include <nvbio/io/utils.h>
#include <nvbio/basic/dna.h>
#include <nvBowtie/bowtie2/cuda/traceback_inl.h>

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

Enumerations
enum	nvbio::bowtie2::cuda::MateType { nvbio::bowtie2::cuda::AnchorMate = 0, nvbio::bowtie2::cuda::OppositeMate = 1 }

Functions
template<typename vector_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	nvbio::bowtie2::cuda::read_cigar_length (const vector_type cigar, const uint32 cigar_len)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE const char *	nvbio::bowtie2::cuda::mate_string (const MateType mate)
template<uint32 ALN_IDX, typename pipeline_type >
void	nvbio::bowtie2::cuda::banded_traceback_best_t (const uint32 count, const uint32 *idx, io::Alignment *best_data, const uint32 best_stride, const uint32 band_len, const pipeline_type &pipeline, const ParamsPOD params)
template<uint32 ALN_IDX, typename pipeline_type >
void	nvbio::bowtie2::cuda::opposite_traceback_best_t (const uint32 count, const uint32 *idx, io::Alignment *best_data, const uint32 best_stride, const pipeline_type &pipeline, const ParamsPOD params)
template<typename pipeline_type >
void	nvbio::bowtie2::cuda::banded_traceback_all_t (const uint32 count, const uint32 *idx, const uint32 buffer_offset, const uint32 buffer_size, io::Alignment *alignments, const uint32 band_len, const pipeline_type &pipeline, const ParamsPOD params)
template<uint32 ALN_IDX, typename scoring_scheme_type , typename pipeline_type >
void	nvbio::bowtie2::cuda::finish_alignment_best_t (const uint32 count, const uint32 *idx, io::Alignment *best_data, const uint32 best_stride, const uint32 band_len, const pipeline_type &pipeline, const scoring_scheme_type scoring_scheme, const ParamsPOD params)
template<uint32 ALN_IDX, typename scoring_scheme_type , typename pipeline_type >
void	nvbio::bowtie2::cuda::finish_opposite_alignment_best_t (const uint32 count, const uint32 *idx, io::Alignment *best_data, const uint32 best_stride, const uint32 band_len, const pipeline_type &pipeline, const scoring_scheme_type scoring_scheme, const ParamsPOD params)
template<typename scoring_scheme_type , typename pipeline_type >
void	nvbio::bowtie2::cuda::finish_alignment_all_t (const uint32 count, const uint32 *idx, const uint32 buffer_offset, const uint32 buffer_size, io::Alignment *alignments, const uint32 band_len, const pipeline_type &pipeline, const scoring_scheme_type scoring_scheme, const ParamsPOD params)