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nvbio::bowtie2::cuda::ReadHitsIndex Struct Reference

Detailed description

This data structure represents a collection of hit arrays bound to a set of reads.
For each read it stores an array of hits of arbitrary length.

Internally, the links from a read to its hits are stored inside a contiguous memory arena
using the following strided layout:
/// ******************************************************
/// *  read0   *  read1  *    ...              *  readN  *
/// ******************************************************
///     count  |   count |    ...              |   count 
/// -----------|---------|---------------------|----------
///     hit0   |   hit0  |    ...              |   hit0  
/// -----------|---------|---------------------|----------
///     hit1   |   hit1  |    ...              |   hit1  
/// -----------|---------|---------------------|----------
///      ...   |    ...  |    ...              |    ...  
/// -----------|---------|---------------------|----------
///     hitM   |   hitM  |    ...              |   hitM  
/// ------------------------------------------------------
In practice, if the arena has size max_size, and the stride is N, one can represent
up to M = max_size / N hits per read.

Definition at line 99 of file scoring_queues.h.

#include <scoring_queues.h>

Public Types

enum  Mode { SingleHitPerRead = 0u, MultipleHitsPerRead = 1u }
typedef thrust::device_vector
< uint32
typedef ReadHitsIndexDeviceView device_view_type

Public Methods

uint64 resize (const uint32 max_size, const bool do_alloc)
void setup (const uint32 n_hits_per_read, const uint32 in_reads)
Mode mode () const
ReadHitsIndexDeviceView device_view ()

Public Members

links_storage_type m_links
 links arena More...
uint32 m_stride
 access stride More...
Mode m_mode
 single/multiple hits mode More...

Member Typedef Documentation

Definition at line 102 of file scoring_queues.h.

Definition at line 101 of file scoring_queues.h.

Member Enumeration Documentation


Definition at line 104 of file scoring_queues.h.

Member Function Documentation

ReadHitsIndexDeviceView nvbio::bowtie2::cuda::ReadHitsIndex::device_view ( )

return a view of the data structure

Definition at line 72 of file scoring_queues_inl.h.

Mode nvbio::bowtie2::cuda::ReadHitsIndex::mode ( ) const

return the queue mode

Definition at line 119 of file scoring_queues.h.

uint64 nvbio::bowtie2::cuda::ReadHitsIndex::resize ( const uint32  max_size,
const bool  do_alloc 

alloc enough storage for max_size hits

Definition at line 35 of file scoring_queues_inl.h.

void nvbio::bowtie2::cuda::ReadHitsIndex::setup ( const uint32  n_hits_per_read,
const uint32  in_reads 

setup the number of input reads

Definition at line 45 of file scoring_queues_inl.h.

Member Data Documentation

links_storage_type nvbio::bowtie2::cuda::ReadHitsIndex::m_links

links arena

Definition at line 126 of file scoring_queues.h.

Mode nvbio::bowtie2::cuda::ReadHitsIndex::m_mode

single/multiple hits mode

Definition at line 128 of file scoring_queues.h.

uint32 nvbio::bowtie2::cuda::ReadHitsIndex::m_stride

access stride

Definition at line 127 of file scoring_queues.h.

The documentation for this struct was generated from the following files: