nvbio::bowtie2::cuda::Aligner Member List

This is the complete list of members for nvbio::bowtie2::cuda::Aligner, including all inherited members.

Aligner()	nvbio::bowtie2::cuda::Aligner	inline
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)	nvbio::bowtie2::cuda::Aligner
band_length(const uint32 max_dist)	nvbio::bowtie2::cuda::Aligner	inlinestatic
batch_number	nvbio::bowtie2::cuda::Aligner
BATCH_SIZE	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)	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)	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)	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)	nvbio::bowtie2::cuda::Aligner
best_data_dptr	nvbio::bowtie2::cuda::Aligner
best_data_dptr_o	nvbio::bowtie2::cuda::Aligner
best_data_dvec	nvbio::bowtie2::cuda::Aligner
best_data_dvec_o	nvbio::bowtie2::cuda::Aligner
buffer_alignments_dptr	nvbio::bowtie2::cuda::Aligner
buffer_alignments_dvec	nvbio::bowtie2::cuda::Aligner
buffer_read_info_dptr	nvbio::bowtie2::cuda::Aligner
buffer_read_info_dvec	nvbio::bowtie2::cuda::Aligner
cigar	nvbio::bowtie2::cuda::Aligner
cigar_coords_dptr	nvbio::bowtie2::cuda::Aligner
cigar_coords_dvec	nvbio::bowtie2::cuda::Aligner
dp_buffer_dptr	nvbio::bowtie2::cuda::Aligner
dp_buffer_dvec	nvbio::bowtie2::cuda::Aligner
flags_dptr	nvbio::bowtie2::cuda::Aligner
flags_dvec	nvbio::bowtie2::cuda::Aligner
fmi_type typedef	nvbio::bowtie2::cuda::Aligner
genome_access_type typedef	nvbio::bowtie2::cuda::Aligner
genome_iterator typedef	nvbio::bowtie2::cuda::Aligner
genome_view_type typedef	nvbio::bowtie2::cuda::Aligner
hit_deques	nvbio::bowtie2::cuda::Aligner
hits_count_scan_dptr	nvbio::bowtie2::cuda::Aligner
hits_count_scan_dvec	nvbio::bowtie2::cuda::Aligner
hits_range_scan_dptr	nvbio::bowtie2::cuda::Aligner
hits_range_scan_dvec	nvbio::bowtie2::cuda::Aligner
hits_stats_dptr	nvbio::bowtie2::cuda::Aligner
hits_stats_dvec	nvbio::bowtie2::cuda::Aligner
hits_stats_hvec	nvbio::bowtie2::cuda::Aligner
ID	nvbio::bowtie2::cuda::Aligner
idx_queue_dptr	nvbio::bowtie2::cuda::Aligner
idx_queue_dvec	nvbio::bowtie2::cuda::Aligner
init(const uint32 id, const uint32 batch_size, const Params &params, const EndType type)	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)	nvbio::bowtie2::cuda::Aligner
keep_stats(const uint32 count, Stats &stats)	nvbio::bowtie2::cuda::Aligner
mapq_dptr	nvbio::bowtie2::cuda::Aligner
mapq_dvec	nvbio::bowtie2::cuda::Aligner
MAX_READ_LEN	nvbio::bowtie2::cuda::Aligner	static
mds	nvbio::bowtie2::cuda::Aligner
opposite_queue_dptr	nvbio::bowtie2::cuda::Aligner
opposite_queue_dvec	nvbio::bowtie2::cuda::Aligner
output_alignments_dptr	nvbio::bowtie2::cuda::Aligner
output_alignments_dvec	nvbio::bowtie2::cuda::Aligner
output_file	nvbio::bowtie2::cuda::Aligner
output_read_info_dptr	nvbio::bowtie2::cuda::Aligner
output_read_info_dvec	nvbio::bowtie2::cuda::Aligner
read_base_type typedef	nvbio::bowtie2::cuda::Aligner
read_batch_type typedef	nvbio::bowtie2::cuda::Aligner
read_qual_type typedef	nvbio::bowtie2::cuda::Aligner
read_storage_type typedef	nvbio::bowtie2::cuda::Aligner
read_view_type typedef	nvbio::bowtie2::cuda::Aligner
reseed_dptr	nvbio::bowtie2::cuda::Aligner
reseed_dvec	nvbio::bowtie2::cuda::Aligner
rfmi_type typedef	nvbio::bowtie2::cuda::Aligner
rseeds_dptr	nvbio::bowtie2::cuda::Aligner
rseeds_dvec	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)	nvbio::bowtie2::cuda::Aligner
scoring_queues	nvbio::bowtie2::cuda::Aligner
seed_queues	nvbio::bowtie2::cuda::Aligner
sort_64_bits(const uint32 count)	nvbio::bowtie2::cuda::Aligner
sort_enactor	nvbio::bowtie2::cuda::Aligner
sort_hi_bits(const uint32 count, const uint32 *keys)	nvbio::bowtie2::cuda::Aligner
sort_inplace(const uint32 count, uint32 *keys)	nvbio::bowtie2::cuda::Aligner
sorting_queue_dvec	nvbio::bowtie2::cuda::Aligner
temp_dvec	nvbio::bowtie2::cuda::Aligner
trys_dptr	nvbio::bowtie2::cuda::Aligner
trys_dvec	nvbio::bowtie2::cuda::Aligner