alignment_utils.h File Reference

#include <nvBowtie/bowtie2/cuda/string_utils.h>
#include <nvBowtie/bowtie2/cuda/params.h>
#include <nvbio/alignment/alignment_base.h>
#include <nvbio/io/alignments.h>
#include <nvbio/io/utils.h>
#include <nvbio/basic/vector_view.h>

Go to the source code of this file.

Classes
struct	nvbio::bowtie2::cuda::detail::Backtracker< vector >
struct	nvbio::bowtie2::cuda::detail::AlignmentStrings< AlignerType, PipelineType >
struct	nvbio::bowtie2::cuda::detail::AlignmentStreamContext< TYPE >
struct	nvbio::bowtie2::cuda::detail::AlignmentStreamContext< SCORE_STREAM >
struct	nvbio::bowtie2::cuda::detail::AlignmentStreamContext< OPPOSITE_SCORE_STREAM >
struct	nvbio::bowtie2::cuda::detail::AlignmentStreamContext< TRACEBACK_STREAM >
struct	nvbio::bowtie2::cuda::detail::AlignmentStreamBase< TYPE, AlignerType, PipelineType >
struct	nvbio::bowtie2::cuda::detail::AlignmentStreamBase< TYPE, AlignerType, PipelineType >::context_type

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

Enumerations
enum	nvbio::bowtie2::cuda::detail::AlignmentStreamType { nvbio::bowtie2::cuda::detail::SCORE_STREAM = 0, nvbio::bowtie2::cuda::detail::OPPOSITE_SCORE_STREAM = 1, nvbio::bowtie2::cuda::detail::TRACEBACK_STREAM = 2 }

Functions
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	nvbio::bowtie2::cuda::detail::frame_opposite_mate (const int policy, const uint32 anchor, const bool anchor_fw, bool &left, bool &fw)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32	nvbio::bowtie2::cuda::detail::compute_target_score (const io::BestPairedAlignments &best, const int32 a_worst_score, const int32 o_worst_score)