aligner.h File Reference

#include <nvBowtie/bowtie2/cuda/defs.h>
#include <nvBowtie/bowtie2/cuda/reads_def.h>
#include <nvBowtie/bowtie2/cuda/fmindex_def.h>
#include <nvBowtie/bowtie2/cuda/seed_hit.h>
#include <nvBowtie/bowtie2/cuda/seed_hit_deque_array.h>
#include <nvBowtie/bowtie2/cuda/scoring_queues.h>
#include <nvBowtie/bowtie2/cuda/params.h>
#include <nvBowtie/bowtie2/cuda/stats.h>
#include <nvBowtie/bowtie2/cuda/mapping.h>
#include <nvbio/io/alignments.h>
#include <nvbio/io/output/output_file.h>
#include <nvbio/io/output/output_batch.h>
#include <nvbio/io/sequence/sequence.h>
#include <nvBowtie/bowtie2/cuda/scoring.h>
#include <nvBowtie/bowtie2/cuda/mapq.h>
#include <nvbio/basic/cuda/arch.h>
#include <nvbio/basic/cuda/sort.h>
#include <nvbio/basic/cuda/host_device_buffer.h>
#include <nvbio/basic/cuda/work_queue.h>
#include <nvbio/basic/timer.h>
#include <nvbio/basic/console.h>
#include <nvbio/basic/options.h>
#include <nvbio/basic/threads.h>
#include <nvbio/basic/html.h>
#include <nvbio/basic/dna.h>
#include <nvbio/basic/vector_array.h>
#include <nvbio/fmindex/bwt.h>
#include <nvbio/fmindex/ssa.h>
#include <nvbio/fmindex/fmindex.h>
#include <nvbio/fmindex/fmindex_device.h>
#include <thrust/host_vector.h>
#include <thrust/device_vector.h>
#include <thrust/scan.h>
#include <thrust/sort.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <vector>
#include <algorithm>
#include <numeric>
#include <functional>

Go to the source code of this file.

Classes
struct	nvbio::bowtie2::cuda::Aligner

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

Functions
void	nvbio::bowtie2::cuda::hits_stats (const uint32 batch_size, const SeedHit *hit_data, const uint32 *hit_counts, uint64 *hit_stats)
void	nvbio::bowtie2::cuda::ring_buffer_to_plain_array (const uint32 *buffer, const uint32 buffer_size, const uint32 begin, const uint32 end, uint32 *output)
void	nvbio::bowtie2::cuda::mark_unaligned (const uint32 n_active_reads, const uint32 *active_reads, const io::Alignment *best_data, uint8 *reseed)
void	nvbio::bowtie2::cuda::mark_discordant (const uint32 n_reads, io::Alignment *anchor_data, io::Alignment *opposite_data, const uint32 stride)