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nvbio::io::DeviceOutputBatchSE Struct Reference

Detailed description

base class for representing a batch of alignment results on the device

Definition at line 47 of file output_batch.h.

#include <output_batch.h>

Public Methods

 DeviceOutputBatchSE (uint32 _count, thrust::device_vector< io::Alignment > &_alignments, DeviceCigarArray _cigar, nvbio::DeviceVectorArray< uint8 > &_mds, thrust::device_vector< uint8 > &_mapq, thrust::device_vector< uint32 > *_read_ids=NULL)
void readback_scores (thrust::host_vector< io::Alignment > &host_alignments) const
void readback_cigars (HostCigarArray &host_cigars) const
void readback_mds (nvbio::HostVectorArray< uint8 > &host_mds) const
void readback_mapq (thrust::host_vector< uint8 > &host_mapq) const
void readback_ids (thrust::host_vector< uint32 > &host_ids) const

Public Members

uint32 count
< io::Alignment > & 
DeviceCigarArray cigar
nvbio::DeviceVectorArray< uint8 > & mds
thrust::device_vector< uint8 > & mapq
thrust::device_vector< uint32 > * read_ids

Constructor & Destructor Documentation

nvbio::io::DeviceOutputBatchSE::DeviceOutputBatchSE ( uint32  _count,
thrust::device_vector< io::Alignment > &  _alignments,
DeviceCigarArray  _cigar,
nvbio::DeviceVectorArray< uint8 > &  _mds,
thrust::device_vector< uint8 > &  _mapq,
thrust::device_vector< uint32 > *  _read_ids = NULL 

Definition at line 58 of file output_batch.h.

Member Function Documentation

void nvbio::io::DeviceOutputBatchSE::readback_cigars ( io::HostCigarArray host_cigar) const

Definition at line 68 of file output_batch.cpp.

void nvbio::io::DeviceOutputBatchSE::readback_ids ( thrust::host_vector< uint32 > &  host_ids) const

Definition at line 87 of file output_batch.cpp.

void nvbio::io::DeviceOutputBatchSE::readback_mapq ( thrust::host_vector< uint8 > &  host_mapq) const

Definition at line 81 of file output_batch.cpp.

void nvbio::io::DeviceOutputBatchSE::readback_mds ( nvbio::HostVectorArray< uint8 > &  host_mds) const

Definition at line 75 of file output_batch.cpp.

void nvbio::io::DeviceOutputBatchSE::readback_scores ( thrust::host_vector< io::Alignment > &  host_alignments) const

Definition at line 61 of file output_batch.cpp.

Member Data Documentation

thrust::device_vector<io::Alignment>& nvbio::io::DeviceOutputBatchSE::alignments

Definition at line 52 of file output_batch.h.

DeviceCigarArray nvbio::io::DeviceOutputBatchSE::cigar

Definition at line 53 of file output_batch.h.

uint32 nvbio::io::DeviceOutputBatchSE::count

Definition at line 50 of file output_batch.h.

thrust::device_vector<uint8>& nvbio::io::DeviceOutputBatchSE::mapq

Definition at line 55 of file output_batch.h.

nvbio::DeviceVectorArray<uint8>& nvbio::io::DeviceOutputBatchSE::mds

Definition at line 54 of file output_batch.h.

thrust::device_vector<uint32>* nvbio::io::DeviceOutputBatchSE::read_ids

Definition at line 56 of file output_batch.h.

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