NVBIO
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Groups Pages
Public Types | Public Methods | Static Public Methods | Public Members | Static Public Members | List of all members
nvbio::bowtie2::cuda::Aligner Struct Reference

Detailed description

Definition at line 78 of file aligner.h.

#include <aligner.h>

Public Types

typedef FMIndexDef::type fmi_type
 
typedef FMIndexDef::type rfmi_type
 
typedef ReadsDef::read_storage_type read_storage_type
 
typedef ReadsDef::read_base_type read_base_type
 
typedef ReadsDef::read_qual_type read_qual_type
 
typedef ReadsDef::read_view_type read_view_type
 
typedef ReadsDef::type read_batch_type
 
typedef io::LdgSequenceDataView genome_view_type
 
typedef io::SequenceDataAccess
< DNA, genome_view_type > 		genome_access_type
 
typedef
genome_access_type::sequence_stream_type 		genome_iterator
 

Public Methods

 Aligner ()
 
bool init (const uint32 id, const uint32 batch_size, const Params &params, const EndType type)
 
void keep_stats (const uint32 count, Stats &stats)
 
template<typename scoring_tag >
void best_approx (const Params &params, const fmi_type fmi, const rfmi_type rfmi, const UberScoringScheme &scoring_scheme, const io::SequenceDataDevice &reference_data, const io::FMIndexDataDevice &driver_data, const io::SequenceDataDevice &read_data, io::HostOutputBatchSE &cpu_batch, Stats &stats)
 
template<typename scoring_tag , typename scoring_scheme_type >
void best_approx_score (const Params &params, const fmi_type fmi, const rfmi_type rfmi, const scoring_scheme_type &scoring_scheme, const io::SequenceDataDevice &reference_data, const io::FMIndexDataDevice &driver_data, const io::SequenceDataDevice &read_data, const uint32 seeding_pass, const uint32 seed_queue_size, const uint32 *seed_queue, Stats &stats)
 
template<typename scoring_tag >
void best_approx (const Params &params, const FMIndexDef::type fmi, const FMIndexDef::type rfmi, const UberScoringScheme &scoring_scheme, const io::SequenceDataDevice &reference_data, const io::FMIndexDataDevice &driver_data, const io::SequenceDataDevice &read_data1, const io::SequenceDataDevice &read_data2, io::HostOutputBatchPE &cpu_batch, Stats &stats)
 
template<typename scoring_tag , typename scoring_scheme_type >
void best_approx_score (const Params &params, const fmi_type fmi, const rfmi_type rfmi, const scoring_scheme_type &scoring_scheme, const io::SequenceDataDevice &reference_data, const io::FMIndexDataDevice &driver_data, const uint32 anchor, const io::SequenceDataDevice &read_data1, const io::SequenceDataDevice &read_data2, const uint32 seeding_pass, const uint32 seed_queue_size, const uint32 *seed_queue, Stats &stats)
 
template<typename scoring_tag >
void all (const Params &params, const fmi_type fmi, const rfmi_type rfmi, const UberScoringScheme &scoring_scheme, const io::SequenceDataDevice &reference_data, const io::FMIndexDataDevice &driver_data, const io::SequenceDataDevice &read_data, io::HostOutputBatchSE &cpu_batch, Stats &stats)
 
template<typename scoring_scheme_type >
void score_all (const Params &params, const fmi_type fmi, const rfmi_type rfmi, const UberScoringScheme &input_scoring_scheme, const scoring_scheme_type &scoring_scheme, const io::SequenceDataDevice &reference_data, const io::FMIndexDataDevice &driver_data, const io::SequenceDataDevice &read_data, io::HostOutputBatchSE &cpu_batch, const uint32 seed_queue_size, const uint32 *seed_queue, Stats &stats, uint64 &total_alignments)
 
std::pair< uint32 *, uint64 * > sort_64_bits (const uint32 count)
 
uint32 * sort_hi_bits (const uint32 count, const uint32 *keys)
 
void sort_inplace (const uint32 count, uint32 *keys)
 
bool init_alloc (const uint32 BATCH_SIZE, const Params &params, const EndType type, bool do_alloc, std::pair< uint64, uint64 > *mem_stats=NULL)
 

Static Public Methods

static uint32 band_length (const uint32 max_dist)
 

Public Members

uint32 ID
 
uint32 BATCH_SIZE
 
thrust::device_vector< uint8 > dp_buffer_dvec
 
uint8 * dp_buffer_dptr
 
SeedHitDequeArray hit_deques
 
nvbio::cuda::PingPongQueues
< uint32 > 		seed_queues
 
ScoringQueues scoring_queues
 
thrust::device_vector< uint32 > idx_queue_dvec
 
uint32 * idx_queue_dptr
 
thrust::device_vector< uint16 > sorting_queue_dvec
 
thrust::device_vector< uint8 > reseed_dvec
 
uint8 * reseed_dptr
 
thrust::device_vector< uint32 > trys_dvec
 
uint32 * trys_dptr
 
thrust::device_vector< uint32 > rseeds_dvec
 
uint32 * rseeds_dptr
 
thrust::device_vector< uint8 > flags_dvec
 
uint8 * flags_dptr
 
nvbio::vector< device_tag, uint8 > temp_dvec
 
thrust::device_vector
< io::Alignment > 		best_data_dvec
 
thrust::device_vector
< io::Alignment > 		best_data_dvec_o
 
io::Alignment * best_data_dptr
 
io::Alignment * best_data_dptr_o
 
thrust::device_vector< uint8 > mapq_dvec
 
uint8 * mapq_dptr
 
thrust::device_vector< uint32 > opposite_queue_dvec
 
uint32 * opposite_queue_dptr
 
thrust::device_vector
< io::Alignment > 		buffer_alignments_dvec
 
io::Alignment * buffer_alignments_dptr
 
thrust::device_vector< uint32 > buffer_read_info_dvec
 
uint32 * buffer_read_info_dptr
 
thrust::device_vector
< io::Alignment > 		output_alignments_dvec
 
io::Alignment * output_alignments_dptr
 
thrust::device_vector< uint32 > output_read_info_dvec
 
uint32 * output_read_info_dptr
 
thrust::device_vector< uint32 > hits_count_scan_dvec
 
uint32 * hits_count_scan_dptr
 
thrust::device_vector< uint64 > hits_range_scan_dvec
 
uint64 * hits_range_scan_dptr
 
nvbio::DeviceVectorArray< uint8 > mds
 
nvbio::DeviceVectorArray
< io::Cigar > 		cigar
 
thrust::device_vector< uint2 > cigar_coords_dvec
 
uint2 * cigar_coords_dptr
 
thrust::device_vector< uint64 > hits_stats_dvec
 
thrust::host_vector< uint64 > hits_stats_hvec
 
uint64 * hits_stats_dptr
 
uint32 batch_number
 
nvbio::cuda::SortEnactor sort_enactor
 
io::OutputFile * output_file
 

Static Public Members

static const uint32 MAX_READ_LEN = MAXIMUM_READ_LENGTH
 

Member Typedef Documentation

typedef FMIndexDef::type nvbio::bowtie2::cuda::Aligner::fmi_type

Definition at line 82 of file aligner.h.

typedef io::SequenceDataAccess<DNA,genome_view_type> nvbio::bowtie2::cuda::Aligner::genome_access_type

Definition at line 92 of file aligner.h.

typedef genome_access_type::sequence_stream_type nvbio::bowtie2::cuda::Aligner::genome_iterator

Definition at line 93 of file aligner.h.

typedef io::LdgSequenceDataView nvbio::bowtie2::cuda::Aligner::genome_view_type

Definition at line 91 of file aligner.h.

typedef ReadsDef::read_base_type nvbio::bowtie2::cuda::Aligner::read_base_type

Definition at line 86 of file aligner.h.

typedef ReadsDef::type nvbio::bowtie2::cuda::Aligner::read_batch_type

Definition at line 89 of file aligner.h.

typedef ReadsDef::read_qual_type nvbio::bowtie2::cuda::Aligner::read_qual_type

Definition at line 87 of file aligner.h.

typedef ReadsDef::read_storage_type nvbio::bowtie2::cuda::Aligner::read_storage_type

Definition at line 85 of file aligner.h.

typedef ReadsDef::read_view_type nvbio::bowtie2::cuda::Aligner::read_view_type

Definition at line 88 of file aligner.h.

typedef FMIndexDef::type nvbio::bowtie2::cuda::Aligner::rfmi_type

Definition at line 83 of file aligner.h.

Constructor & Destructor Documentation

nvbio::bowtie2::cuda::Aligner::Aligner ( )
inline

Definition at line 176 of file aligner.h.

Member Function Documentation

template<typename scoring_tag >
void nvbio::bowtie2::cuda::Aligner::all ( const Params &  params,
const fmi_type  fmi,
const rfmi_type  rfmi,
const UberScoringScheme &  scoring_scheme,
const io::SequenceDataDevice &  reference_data,
const io::FMIndexDataDevice &  driver_data,
const io::SequenceDataDevice &  read_data,
io::HostOutputBatchSE &  cpu_batch,
Stats &  stats 
)

Definition at line 49 of file aligner_all.h.

static uint32 nvbio::bowtie2::cuda::Aligner::band_length ( const uint32  max_dist)
inlinestatic

Definition at line 165 of file aligner.h.

template<typename scoring_tag >
void nvbio::bowtie2::cuda::Aligner::best_approx ( const Params &  params,
const fmi_type  fmi,
const rfmi_type  rfmi,
const UberScoringScheme &  scoring_scheme,
const io::SequenceDataDevice &  reference_data,
const io::FMIndexDataDevice &  driver_data,
const io::SequenceDataDevice &  read_data,
io::HostOutputBatchSE &  cpu_batch,
Stats &  stats 
)

Definition at line 85 of file aligner_best_approx.h.

template<typename scoring_tag >
void nvbio::bowtie2::cuda::Aligner::best_approx ( const Params &  params,
const FMIndexDef::type  fmi,
const FMIndexDef::type  rfmi,
const UberScoringScheme &  scoring_scheme,
const io::SequenceDataDevice &  reference_data,
const io::FMIndexDataDevice &  driver_data,
const io::SequenceDataDevice &  read_data1,
const io::SequenceDataDevice &  read_data2,
io::HostOutputBatchPE &  cpu_batch,
Stats &  stats 
)

Definition at line 100 of file aligner_best_approx_paired.h.

template<typename scoring_tag , typename scoring_scheme_type >
void nvbio::bowtie2::cuda::Aligner::best_approx_score ( const Params &  params,
const fmi_type  fmi,
const rfmi_type  rfmi,
const scoring_scheme_type &  scoring_scheme,
const io::SequenceDataDevice &  reference_data,
const io::FMIndexDataDevice &  driver_data,
const io::SequenceDataDevice &  read_data,
const uint32  seeding_pass,
const uint32  seed_queue_size,
const uint32 *  seed_queue,
Stats &  stats 
)

Definition at line 525 of file aligner_best_approx.h.

template<typename scoring_tag , typename scoring_scheme_type >
void nvbio::bowtie2::cuda::Aligner::best_approx_score ( const Params &  params,
const fmi_type  fmi,
const rfmi_type  rfmi,
const scoring_scheme_type &  scoring_scheme,
const io::SequenceDataDevice &  reference_data,
const io::FMIndexDataDevice &  driver_data,
const uint32  anchor,
const io::SequenceDataDevice &  read_data1,
const io::SequenceDataDevice &  read_data2,
const uint32  seeding_pass,
const uint32  seed_queue_size,
const uint32 *  seed_queue,
Stats &  stats 
)

Definition at line 821 of file aligner_best_approx_paired.h.

bool nvbio::bowtie2::cuda::Aligner::init ( const uint32  id,
const uint32  batch_size,
const Params &  params,
const EndType  type 
)
bool nvbio::bowtie2::cuda::Aligner::init_alloc ( const uint32  BATCH_SIZE,
const Params &  params,
const EndType  type,
bool  do_alloc,
std::pair< uint64, uint64 > *  mem_stats = NULL 
)
void nvbio::bowtie2::cuda::Aligner::keep_stats ( const uint32  count,
Stats &  stats 
)
template<typename scoring_scheme_type >
void nvbio::bowtie2::cuda::Aligner::score_all ( const Params &  params,
const fmi_type  fmi,
const rfmi_type  rfmi,
const UberScoringScheme &  input_scoring_scheme,
const scoring_scheme_type &  scoring_scheme,
const io::SequenceDataDevice &  reference_data,
const io::FMIndexDataDevice &  driver_data,
const io::SequenceDataDevice &  read_data,
io::HostOutputBatchSE &  cpu_batch,
const uint32  seed_queue_size,
const uint32 *  seed_queue,
Stats &  stats,
uint64 &  total_alignments 
)

Definition at line 278 of file aligner_all.h.

std::pair<uint32*,uint64*> nvbio::bowtie2::cuda::Aligner::sort_64_bits ( const uint32  count)
uint32* nvbio::bowtie2::cuda::Aligner::sort_hi_bits ( const uint32  count,
const uint32 *  keys 
)
void nvbio::bowtie2::cuda::Aligner::sort_inplace ( const uint32  count,
uint32 *  keys 
)

Member Data Documentation

uint32 nvbio::bowtie2::cuda::Aligner::batch_number

Definition at line 157 of file aligner.h.

uint32 nvbio::bowtie2::cuda::Aligner::BATCH_SIZE

Definition at line 97 of file aligner.h.

io::Alignment* nvbio::bowtie2::cuda::Aligner::best_data_dptr

Definition at line 123 of file aligner.h.

io::Alignment* nvbio::bowtie2::cuda::Aligner::best_data_dptr_o

Definition at line 124 of file aligner.h.

thrust::device_vector<io::Alignment> nvbio::bowtie2::cuda::Aligner::best_data_dvec

Definition at line 121 of file aligner.h.

thrust::device_vector<io::Alignment> nvbio::bowtie2::cuda::Aligner::best_data_dvec_o

Definition at line 122 of file aligner.h.

io::Alignment* nvbio::bowtie2::cuda::Aligner::buffer_alignments_dptr

Definition at line 134 of file aligner.h.

thrust::device_vector<io::Alignment> nvbio::bowtie2::cuda::Aligner::buffer_alignments_dvec

Definition at line 133 of file aligner.h.

uint32* nvbio::bowtie2::cuda::Aligner::buffer_read_info_dptr

Definition at line 136 of file aligner.h.

thrust::device_vector<uint32> nvbio::bowtie2::cuda::Aligner::buffer_read_info_dvec

Definition at line 135 of file aligner.h.

nvbio::DeviceVectorArray<io::Cigar> nvbio::bowtie2::cuda::Aligner::cigar

Definition at line 149 of file aligner.h.

uint2* nvbio::bowtie2::cuda::Aligner::cigar_coords_dptr

Definition at line 151 of file aligner.h.

thrust::device_vector<uint2> nvbio::bowtie2::cuda::Aligner::cigar_coords_dvec

Definition at line 150 of file aligner.h.

uint8* nvbio::bowtie2::cuda::Aligner::dp_buffer_dptr

Definition at line 100 of file aligner.h.

thrust::device_vector<uint8> nvbio::bowtie2::cuda::Aligner::dp_buffer_dvec

Definition at line 99 of file aligner.h.

uint8* nvbio::bowtie2::cuda::Aligner::flags_dptr

Definition at line 118 of file aligner.h.

thrust::device_vector<uint8> nvbio::bowtie2::cuda::Aligner::flags_dvec

Definition at line 117 of file aligner.h.

SeedHitDequeArray nvbio::bowtie2::cuda::Aligner::hit_deques

Definition at line 102 of file aligner.h.

uint32* nvbio::bowtie2::cuda::Aligner::hits_count_scan_dptr

Definition at line 143 of file aligner.h.

thrust::device_vector<uint32> nvbio::bowtie2::cuda::Aligner::hits_count_scan_dvec

Definition at line 142 of file aligner.h.

uint64* nvbio::bowtie2::cuda::Aligner::hits_range_scan_dptr

Definition at line 145 of file aligner.h.

thrust::device_vector<uint64> nvbio::bowtie2::cuda::Aligner::hits_range_scan_dvec

Definition at line 144 of file aligner.h.

uint64* nvbio::bowtie2::cuda::Aligner::hits_stats_dptr

Definition at line 155 of file aligner.h.

thrust::device_vector<uint64> nvbio::bowtie2::cuda::Aligner::hits_stats_dvec

Definition at line 153 of file aligner.h.

thrust::host_vector<uint64> nvbio::bowtie2::cuda::Aligner::hits_stats_hvec

Definition at line 154 of file aligner.h.

uint32 nvbio::bowtie2::cuda::Aligner::ID

Definition at line 96 of file aligner.h.

uint32* nvbio::bowtie2::cuda::Aligner::idx_queue_dptr

Definition at line 108 of file aligner.h.

thrust::device_vector<uint32> nvbio::bowtie2::cuda::Aligner::idx_queue_dvec

Definition at line 107 of file aligner.h.

uint8* nvbio::bowtie2::cuda::Aligner::mapq_dptr

Definition at line 126 of file aligner.h.

thrust::device_vector<uint8> nvbio::bowtie2::cuda::Aligner::mapq_dvec

Definition at line 125 of file aligner.h.

const uint32 nvbio::bowtie2::cuda::Aligner::MAX_READ_LEN = MAXIMUM_READ_LENGTH
static

Definition at line 80 of file aligner.h.

nvbio::DeviceVectorArray<uint8> nvbio::bowtie2::cuda::Aligner::mds

Definition at line 148 of file aligner.h.

uint32* nvbio::bowtie2::cuda::Aligner::opposite_queue_dptr

Definition at line 130 of file aligner.h.

thrust::device_vector<uint32> nvbio::bowtie2::cuda::Aligner::opposite_queue_dvec

Definition at line 129 of file aligner.h.

io::Alignment* nvbio::bowtie2::cuda::Aligner::output_alignments_dptr

Definition at line 138 of file aligner.h.

thrust::device_vector<io::Alignment> nvbio::bowtie2::cuda::Aligner::output_alignments_dvec

Definition at line 137 of file aligner.h.

io::OutputFile* nvbio::bowtie2::cuda::Aligner::output_file

Definition at line 163 of file aligner.h.

uint32* nvbio::bowtie2::cuda::Aligner::output_read_info_dptr

Definition at line 140 of file aligner.h.

thrust::device_vector<uint32> nvbio::bowtie2::cuda::Aligner::output_read_info_dvec

Definition at line 139 of file aligner.h.

uint8* nvbio::bowtie2::cuda::Aligner::reseed_dptr

Definition at line 112 of file aligner.h.

thrust::device_vector<uint8> nvbio::bowtie2::cuda::Aligner::reseed_dvec

Definition at line 111 of file aligner.h.

uint32* nvbio::bowtie2::cuda::Aligner::rseeds_dptr

Definition at line 116 of file aligner.h.

thrust::device_vector<uint32> nvbio::bowtie2::cuda::Aligner::rseeds_dvec

Definition at line 115 of file aligner.h.

ScoringQueues nvbio::bowtie2::cuda::Aligner::scoring_queues

Definition at line 105 of file aligner.h.

nvbio::cuda::PingPongQueues<uint32> nvbio::bowtie2::cuda::Aligner::seed_queues

Definition at line 104 of file aligner.h.

nvbio::cuda::SortEnactor nvbio::bowtie2::cuda::Aligner::sort_enactor

Definition at line 159 of file aligner.h.

thrust::device_vector<uint16> nvbio::bowtie2::cuda::Aligner::sorting_queue_dvec

Definition at line 109 of file aligner.h.

nvbio::vector<device_tag,uint8> nvbio::bowtie2::cuda::Aligner::temp_dvec

Definition at line 119 of file aligner.h.

uint32* nvbio::bowtie2::cuda::Aligner::trys_dptr

Definition at line 114 of file aligner.h.

thrust::device_vector<uint32> nvbio::bowtie2::cuda::Aligner::trys_dvec

Definition at line 113 of file aligner.h.

The documentation for this struct was generated from the following files:
Generated on Wed Feb 25 2015 08:34:08 for NVBIO by   doxygen 1.8.4