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Traceback
nvBowtie

Detailed Description

Modules

 TracebackDetail
 

Enumerations

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

Functions

void nvbio::bowtie2::cuda::banded_traceback_best (const uint32 aln_idx, const uint32 count, const uint32 *idx, io::Alignment *best_data, const uint32 best_stride, const uint32 band_len, const TracebackPipelineState< EditDistanceScoringScheme > &pipeline, const ParamsPOD &params)
 
void nvbio::bowtie2::cuda::banded_traceback_best (const uint32 aln_idx, const uint32 count, const uint32 *idx, io::Alignment *best_data, const uint32 best_stride, const uint32 band_len, const TracebackPipelineState< SmithWatermanScoringScheme<> > &pipeline, const ParamsPOD &params)
 
void nvbio::bowtie2::cuda::opposite_traceback_best (const uint32 aln_idx, const uint32 count, const uint32 *idx, io::Alignment *best_data, const uint32 best_stride, const TracebackPipelineState< EditDistanceScoringScheme > &pipeline, const ParamsPOD &params)
 
void nvbio::bowtie2::cuda::opposite_traceback_best (const uint32 aln_idx, const uint32 count, const uint32 *idx, io::Alignment *best_data, const uint32 best_stride, const TracebackPipelineState< SmithWatermanScoringScheme<> > &pipeline, const ParamsPOD &params)
 
void nvbio::bowtie2::cuda::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 AllMappingPipelineState< EditDistanceScoringScheme > &pipeline, const ParamsPOD &params)
 
void nvbio::bowtie2::cuda::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 AllMappingPipelineState< SmithWatermanScoringScheme<> > &pipeline, const ParamsPOD &params)
 
void nvbio::bowtie2::cuda::finish_alignment_best (const uint32 aln_idx, const uint32 count, const uint32 *idx, io::Alignment *best_data, const uint32 best_stride, const uint32 band_len, const TracebackPipelineState< EditDistanceScoringScheme > &pipeline, const SmithWatermanScoringScheme<> scoring_scheme, const ParamsPOD &params)
 
void nvbio::bowtie2::cuda::finish_alignment_best (const uint32 aln_idx, const uint32 count, const uint32 *idx, io::Alignment *best_data, const uint32 best_stride, const uint32 band_len, const TracebackPipelineState< SmithWatermanScoringScheme<> > &pipeline, const SmithWatermanScoringScheme<> scoring_scheme, const ParamsPOD &params)
 
void nvbio::bowtie2::cuda::finish_opposite_alignment_best (const uint32 aln_idx, const uint32 count, const uint32 *idx, io::Alignment *best_data, const uint32 best_stride, const uint32 band_len, const TracebackPipelineState< EditDistanceScoringScheme > &pipeline, const SmithWatermanScoringScheme<> scoring_scheme, const ParamsPOD &params)
 
void nvbio::bowtie2::cuda::finish_opposite_alignment_best (const uint32 aln_idx, const uint32 count, const uint32 *idx, io::Alignment *best_data, const uint32 best_stride, const uint32 band_len, const TracebackPipelineState< SmithWatermanScoringScheme<> > &pipeline, const SmithWatermanScoringScheme<> scoring_scheme, const ParamsPOD &params)
 
void nvbio::bowtie2::cuda::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 AllMappingPipelineState< EditDistanceScoringScheme > &pipeline, const SmithWatermanScoringScheme<> scoring_scheme, const ParamsPOD &params)
 
void nvbio::bowtie2::cuda::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 AllMappingPipelineState< SmithWatermanScoringScheme<> > &pipeline, const SmithWatermanScoringScheme<> scoring_scheme, const ParamsPOD &params)
 
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)
 

Enumeration Type Documentation

enum nvbio::bowtie2::cuda::MateType
Enumerator
AnchorMate 
OppositeMate 

Definition at line 67 of file traceback_impl.h.

Function Documentation

void nvbio::bowtie2::cuda::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 AllMappingPipelineState< EditDistanceScoringScheme > &  pipeline,
const ParamsPOD &  params 
)

execute a batch of banded-alignment traceback calculations

void nvbio::bowtie2::cuda::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 AllMappingPipelineState< SmithWatermanScoringScheme<> > &  pipeline,
const ParamsPOD &  params 
)

execute a batch of banded-alignment traceback calculations

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 
)

execute a batch of banded-alignment traceback calculations

Definition at line 912 of file traceback_inl.h.

void nvbio::bowtie2::cuda::banded_traceback_best ( const uint32  aln_idx,
const uint32  count,
const uint32 *  idx,
io::Alignment *  best_data,
const uint32  best_stride,
const uint32  band_len,
const TracebackPipelineState< EditDistanceScoringScheme > &  pipeline,
const ParamsPOD &  params 
)

execute a batch of banded-alignment traceback calculations

void nvbio::bowtie2::cuda::banded_traceback_best ( const uint32  aln_idx,
const uint32  count,
const uint32 *  idx,
io::Alignment *  best_data,
const uint32  best_stride,
const uint32  band_len,
const TracebackPipelineState< SmithWatermanScoringScheme<> > &  pipeline,
const ParamsPOD &  params 
)

execute a batch of banded-alignment traceback calculations

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 
)

execute a batch of banded-alignment traceback calculations

Definition at line 833 of file traceback_inl.h.

void nvbio::bowtie2::cuda::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 AllMappingPipelineState< EditDistanceScoringScheme > &  pipeline,
const SmithWatermanScoringScheme<>  scoring_scheme,
const ParamsPOD &  params 
)

finish a batch of alignment calculations, all-mapping

void nvbio::bowtie2::cuda::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 AllMappingPipelineState< SmithWatermanScoringScheme<> > &  pipeline,
const SmithWatermanScoringScheme<>  scoring_scheme,
const ParamsPOD &  params 
)

finish a batch of alignment calculations, all-mapping

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 
)

finish a batch of alignment calculations, all-mapping

Definition at line 1006 of file traceback_inl.h.

void nvbio::bowtie2::cuda::finish_alignment_best ( const uint32  aln_idx,
const uint32  count,
const uint32 *  idx,
io::Alignment *  best_data,
const uint32  best_stride,
const uint32  band_len,
const TracebackPipelineState< EditDistanceScoringScheme > &  pipeline,
const SmithWatermanScoringScheme<>  scoring_scheme,
const ParamsPOD &  params 
)

finish a batch of alignment calculations

void nvbio::bowtie2::cuda::finish_alignment_best ( const uint32  aln_idx,
const uint32  count,
const uint32 *  idx,
io::Alignment *  best_data,
const uint32  best_stride,
const uint32  band_len,
const TracebackPipelineState< SmithWatermanScoringScheme<> > &  pipeline,
const SmithWatermanScoringScheme<>  scoring_scheme,
const ParamsPOD &  params 
)

finish a batch of alignment calculations

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 
)

finish a batch of alignment calculations

Definition at line 954 of file traceback_inl.h.

void nvbio::bowtie2::cuda::finish_opposite_alignment_best ( const uint32  aln_idx,
const uint32  count,
const uint32 *  idx,
io::Alignment *  best_data,
const uint32  best_stride,
const uint32  band_len,
const TracebackPipelineState< EditDistanceScoringScheme > &  pipeline,
const SmithWatermanScoringScheme<>  scoring_scheme,
const ParamsPOD &  params 
)

finish a batch of opposite alignment calculations

void nvbio::bowtie2::cuda::finish_opposite_alignment_best ( const uint32  aln_idx,
const uint32  count,
const uint32 *  idx,
io::Alignment *  best_data,
const uint32  best_stride,
const uint32  band_len,
const TracebackPipelineState< SmithWatermanScoringScheme<> > &  pipeline,
const SmithWatermanScoringScheme<>  scoring_scheme,
const ParamsPOD &  params 
)

finish a batch of opposite alignment calculations

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 
)

finish a batch of opposite alignment calculations

Definition at line 980 of file traceback_inl.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE const char* nvbio::bowtie2::cuda::mate_string ( const MateType  mate)

Definition at line 74 of file traceback_impl.h.

void nvbio::bowtie2::cuda::opposite_traceback_best ( const uint32  aln_idx,
const uint32  count,
const uint32 *  idx,
io::Alignment *  best_data,
const uint32  best_stride,
const TracebackPipelineState< EditDistanceScoringScheme > &  pipeline,
const ParamsPOD &  params 
)

execute a batch of opposite alignment traceback calculations

void nvbio::bowtie2::cuda::opposite_traceback_best ( const uint32  aln_idx,
const uint32  count,
const uint32 *  idx,
io::Alignment *  best_data,
const uint32  best_stride,
const TracebackPipelineState< SmithWatermanScoringScheme<> > &  pipeline,
const ParamsPOD &  params 
)

execute a batch of opposite alignment traceback calculations

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 
)

execute a batch of opposite alignment traceback calculations

Definition at line 874 of file traceback_inl.h.

template<typename vector_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::bowtie2::cuda::read_cigar_length ( const vector_type  cigar,
const uint32  cigar_len 
)

Definition at line 53 of file traceback_impl.h.

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