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TracebackDetail

Detailed Description

Classes

struct  nvbio::bowtie2::cuda::detail::BestTracebackStream< ALN_IDX, AlignerType, PipelineType >
 
struct  nvbio::bowtie2::cuda::detail::AllTracebackStream< AlignerType, PipelineType >
 

Functions

template<uint32 ALN_IDX, typename aligner_type , typename pipeline_type >
void nvbio::bowtie2::cuda::detail::banded_traceback_best (const MateType mate_type, const uint32 count, const uint32 *idx, io::Alignment *best_data, const uint32 best_stride, const uint32 band_len, const pipeline_type &pipeline, const aligner_type aligner, const ParamsPOD params)
 
template<uint32 ALN_IDX, typename aligner_type , typename pipeline_type >
void nvbio::bowtie2::cuda::detail::traceback_best (const MateType mate_type, const uint32 count, const uint32 *idx, io::Alignment *best_data, const uint32 best_stride, const pipeline_type &pipeline, const aligner_type aligner, const ParamsPOD params)
 
template<typename aligner_type , typename pipeline_type >
void nvbio::bowtie2::cuda::detail::banded_traceback_all (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 aligner_type aligner, const ParamsPOD params)
 
template<typename stream_type , typename scheme_type , typename pipeline_type >
__global__ void nvbio::bowtie2::cuda::detail::finish_alignment_kernel (stream_type stream, pipeline_type pipeline, const scheme_type scoring_scheme, const ParamsPOD params)
 
template<uint32 ALN_IDX, typename scheme_type , typename pipeline_type >
void nvbio::bowtie2::cuda::detail::finish_alignment_best (const MateType mate_type, const uint32 count, const uint32 *idx, io::Alignment *best_data, const uint32 best_stride, const uint32 band_len, const pipeline_type &pipeline, const scheme_type scoring_scheme, const ParamsPOD params)
 
template<typename scheme_type , typename pipeline_type >
void nvbio::bowtie2::cuda::detail::finish_alignment_all (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 scheme_type scoring_scheme, const ParamsPOD params)
 

Function Documentation

template<typename aligner_type , typename pipeline_type >
void nvbio::bowtie2::cuda::detail::banded_traceback_all ( 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 aligner_type  aligner,
const ParamsPOD  params 
)

dispatch the execution of a batch of single-ended banded-alignment traceback calculations

Definition at line 461 of file traceback_inl.h.

template<uint32 ALN_IDX, typename aligner_type , typename pipeline_type >
void nvbio::bowtie2::cuda::detail::banded_traceback_best ( const MateType  mate_type,
const uint32  count,
const uint32 *  idx,
io::Alignment *  best_data,
const uint32  best_stride,
const uint32  band_len,
const pipeline_type &  pipeline,
const aligner_type  aligner,
const ParamsPOD  params 
)

dispatch the execution of a batch of single-ended banded-alignment traceback calculations

Definition at line 205 of file traceback_inl.h.

template<typename scheme_type , typename pipeline_type >
void nvbio::bowtie2::cuda::detail::finish_alignment_all ( 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 scheme_type  scoring_scheme,
const ParamsPOD  params 
)

finish computing the final alignments, i.e. computing the MD strings and the final scores (given the CIGARs)

Definition at line 778 of file traceback_inl.h.

template<uint32 ALN_IDX, typename scheme_type , typename pipeline_type >
void nvbio::bowtie2::cuda::detail::finish_alignment_best ( const MateType  mate_type,
const uint32  count,
const uint32 *  idx,
io::Alignment *  best_data,
const uint32  best_stride,
const uint32  band_len,
const pipeline_type &  pipeline,
const scheme_type  scoring_scheme,
const ParamsPOD  params 
)

finish computing the final alignments, i.e. computing the MD strings and the final scores (given the CIGARs)

Definition at line 729 of file traceback_inl.h.

template<typename stream_type , typename scheme_type , typename pipeline_type >
__global__ void nvbio::bowtie2::cuda::detail::finish_alignment_kernel ( stream_type  stream,
pipeline_type  pipeline,
const scheme_type  scoring_scheme,
const ParamsPOD  params 
)

finish computing the final alignments, i.e. computing the MD strings and the final scores (given the CIGARs)

Definition at line 524 of file traceback_inl.h.

template<uint32 ALN_IDX, typename aligner_type , typename pipeline_type >
void nvbio::bowtie2::cuda::detail::traceback_best ( const MateType  mate_type,
const uint32  count,
const uint32 *  idx,
io::Alignment *  best_data,
const uint32  best_stride,
const pipeline_type &  pipeline,
const aligner_type  aligner,
const ParamsPOD  params 
)

dispatch the execution of a batch of full DP alignment traceback calculations

Definition at line 267 of file traceback_inl.h.