cusbf::detail::FastxPipelineState Class Reference

Public Member Functions
	FastxPipelineState ()=default
	FastxPipelineState (const FastxPipelineState &)=delete
FastxPipelineState &	operator= (const FastxPipelineState &)=delete
	FastxPipelineState (FastxPipelineState &&) noexcept=default
FastxPipelineState &	operator= (FastxPipelineState &&) noexcept=default
	~FastxPipelineState ()=default
thrust::device_vector< char > &	sequence_device () noexcept
const thrust::device_vector< char > &	sequence_device () const noexcept
thrust::device_vector< uint64_t > &	dense_packed_words_device () noexcept
const thrust::device_vector< uint64_t > &	dense_packed_words_device () const noexcept
thrust::device_vector< uint8_t > &	result_buffer_device () noexcept
const thrust::device_vector< uint8_t > &	result_buffer_device () const noexcept
thrust::device_vector< QueryLayoutRecord > &	query_layout_records_device () noexcept
const thrust::device_vector< QueryLayoutRecord > &	query_layout_records_device () const noexcept
thrust::device_vector< uint64_t > &	record_positive_kmers_device () noexcept
const thrust::device_vector< uint64_t > &	record_positive_kmers_device () const noexcept
FastxPinnedSequenceBuffer &	normalized_sequence_ping (size_t ping) noexcept
const FastxPinnedSequenceBuffer &	normalized_sequence_ping (size_t ping) const noexcept
std::vector< NormalizedRecord > &	normalized_records_ping (size_t ping) noexcept
const std::vector< NormalizedRecord > &	normalized_records_ping (size_t ping) const noexcept
std::string &	normalized_sequence_scratch () noexcept
const std::string &	normalized_sequence_scratch () const noexcept
std::vector< NormalizedRecord > &	normalized_records_scratch () noexcept
const std::vector< NormalizedRecord > &	normalized_records_scratch () const noexcept
std::vector< uint64_t > &	record_positive_kmers_scratch () noexcept
const std::vector< uint64_t > &	record_positive_kmers_scratch () const noexcept
std::vector< uint8_t > &	result_hits_scratch () noexcept
const std::vector< uint8_t > &	result_hits_scratch () const noexcept
void	ensure_sequence_capacity (uint64_t bases)
void	ensure_dense_packed_capacity (uint64_t words)
void	ensure_result_capacity (uint64_t kmers)
Result< void >	stage_sequence (std::span< const char > sequence, cuda::stream_ref stream)
Result< device_span< const char > >	staged_sequence_view (std::span< const char > sequence, cuda::stream_ref stream)
Result< void >	stage_dense_packed (std::span< const uint64_t > words, cuda::stream_ref stream)
Result< device_span< const uint64_t > >	staged_dense_packed_view (std::span< const uint64_t > words, cuda::stream_ref stream)
Result< device_span< const char > >	stage_sequence_ping (size_t ping, std::string_view sequence, cuda::stream_ref stream)
void	release_host_pings ()
void	release_host_scratch ()
void	release_device_staging ()
void	release_all ()
void	shrink_host_scratch ()
void	shrink_device_staging ()
void	shrink_all ()

Detailed Description

Definition at line 23 of file fastx_pipeline_state.cuh.

Constructor & Destructor Documentation

FastxPipelineState() [1/3]

cusbf::detail::FastxPipelineState::FastxPipelineState ( )

default

FastxPipelineState() [2/3]

cusbf::detail::FastxPipelineState::FastxPipelineState ( const FastxPipelineState &  )

delete

FastxPipelineState() [3/3]

cusbf::detail::FastxPipelineState::FastxPipelineState ( FastxPipelineState &&  )

defaultnoexcept

~FastxPipelineState()

cusbf::detail::FastxPipelineState::~FastxPipelineState ( )

default

Member Function Documentation

dense_packed_words_device() [1/2]

const thrust::device_vector< uint64_t > & cusbf::detail::FastxPipelineState::dense_packed_words_device ( ) const

inlinenoexcept

Definition at line 45 of file fastx_pipeline_state.cuh.

                                               {
        return d_dense_packed_words_;
    }

dense_packed_words_device() [2/2]

thrust::device_vector< uint64_t > & cusbf::detail::FastxPipelineState::dense_packed_words_device ( )

inlinenoexcept

Definition at line 40 of file fastx_pipeline_state.cuh.

                                                                                      {
        return d_dense_packed_words_;
    }

ensure_dense_packed_capacity()

void cusbf::detail::FastxPipelineState::ensure_dense_packed_capacity ( uint64_t  words )

inline

Definition at line 133 of file fastx_pipeline_state.cuh.

                                                      {
        if (words > d_dense_packed_words_.size()) {
            d_dense_packed_words_.resize(words);
        }
    }

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ensure_result_capacity()

void cusbf::detail::FastxPipelineState::ensure_result_capacity ( uint64_t  kmers )

inline

Definition at line 139 of file fastx_pipeline_state.cuh.

                                                {
        if (kmers > d_resultBuffer_.size()) {
            d_resultBuffer_.resize(kmers);
        }
    }

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ensure_sequence_capacity()

void cusbf::detail::FastxPipelineState::ensure_sequence_capacity ( uint64_t  bases )

inline

Definition at line 127 of file fastx_pipeline_state.cuh.

                                                  {
        if (bases > d_sequence_.size()) {
            d_sequence_.resize(bases);
        }
    }

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normalized_records_ping() [1/2]

const std::vector< NormalizedRecord > & cusbf::detail::FastxPipelineState::normalized_records_ping ( size_t  ping ) const

inlinenoexcept

Definition at line 89 of file fastx_pipeline_state.cuh.

                     {
        return normalized_records_pings_[ping & 1U];
    }

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normalized_records_ping() [2/2]

std::vector< NormalizedRecord > & cusbf::detail::FastxPipelineState::normalized_records_ping ( size_t  ping )

inlinenoexcept

Definition at line 85 of file fastx_pipeline_state.cuh.

                                                                                             {
        return normalized_records_pings_[ping & 1U];
    }

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normalized_records_scratch() [1/2]

const std::vector< NormalizedRecord > & cusbf::detail::FastxPipelineState::normalized_records_scratch ( ) const

inlinenoexcept

Definition at line 107 of file fastx_pipeline_state.cuh.

                                                                                                 {
        return normalized_records_scratch_;
    }

normalized_records_scratch() [2/2]

std::vector< NormalizedRecord > & cusbf::detail::FastxPipelineState::normalized_records_scratch ( )

inlinenoexcept

Definition at line 103 of file fastx_pipeline_state.cuh.

                                                                                     {
        return normalized_records_scratch_;
    }

normalized_sequence_ping() [1/2]

const FastxPinnedSequenceBuffer & cusbf::detail::FastxPipelineState::normalized_sequence_ping ( size_t  ping ) const

inlinenoexcept

Definition at line 79 of file fastx_pipeline_state.cuh.

                     {
        return normalized_sequence_pings_[ping & 1U];
    }

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normalized_sequence_ping() [2/2]

FastxPinnedSequenceBuffer & cusbf::detail::FastxPipelineState::normalized_sequence_ping ( size_t  ping )

inlinenoexcept

Definition at line 75 of file fastx_pipeline_state.cuh.

                                                                                            {
        return normalized_sequence_pings_[ping & 1U];
    }

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normalized_sequence_scratch() [1/2]

const std::string & cusbf::detail::FastxPipelineState::normalized_sequence_scratch ( ) const

inlinenoexcept

Definition at line 99 of file fastx_pipeline_state.cuh.

                                                                                {
        return normalized_sequence_scratch_;
    }

normalized_sequence_scratch() [2/2]

std::string & cusbf::detail::FastxPipelineState::normalized_sequence_scratch ( )

inlinenoexcept

Definition at line 95 of file fastx_pipeline_state.cuh.

                                                                    {
        return normalized_sequence_scratch_;
    }

operator=() [1/2]

FastxPipelineState & cusbf::detail::FastxPipelineState::operator= ( const FastxPipelineState &  )

delete

operator=() [2/2]

FastxPipelineState & cusbf::detail::FastxPipelineState::operator= ( FastxPipelineState &&  )

defaultnoexcept

query_layout_records_device() [1/2]

const thrust::device_vector< QueryLayoutRecord > & cusbf::detail::FastxPipelineState::query_layout_records_device ( ) const

inlinenoexcept

Definition at line 62 of file fastx_pipeline_state.cuh.

                                                 {
        return d_query_layout_records_;
    }

query_layout_records_device() [2/2]

thrust::device_vector< QueryLayoutRecord > & cusbf::detail::FastxPipelineState::query_layout_records_device ( )

inlinenoexcept

Definition at line 57 of file fastx_pipeline_state.cuh.

                                                                                                 {
        return d_query_layout_records_;
    }

record_positive_kmers_device() [1/2]

const thrust::device_vector< uint64_t > & cusbf::detail::FastxPipelineState::record_positive_kmers_device ( ) const

inlinenoexcept

Definition at line 71 of file fastx_pipeline_state.cuh.

                                                  {
        return d_record_positive_kmers_;
    }

record_positive_kmers_device() [2/2]

thrust::device_vector< uint64_t > & cusbf::detail::FastxPipelineState::record_positive_kmers_device ( )

inlinenoexcept

Definition at line 66 of file fastx_pipeline_state.cuh.

                                                                                         {
        return d_record_positive_kmers_;
    }

record_positive_kmers_scratch() [1/2]

const std::vector< uint64_t > & cusbf::detail::FastxPipelineState::record_positive_kmers_scratch ( ) const

inlinenoexcept

Definition at line 115 of file fastx_pipeline_state.cuh.

                                                                                            {
        return record_positive_kmers_scratch_;
    }

record_positive_kmers_scratch() [2/2]

std::vector< uint64_t > & cusbf::detail::FastxPipelineState::record_positive_kmers_scratch ( )

inlinenoexcept

Definition at line 111 of file fastx_pipeline_state.cuh.

                                                                                {
        return record_positive_kmers_scratch_;
    }

release_all()

void cusbf::detail::FastxPipelineState::release_all ( )

inline

Definition at line 230 of file fastx_pipeline_state.cuh.

                       {
        release_host_pings();
        release_host_scratch();
        release_device_staging();
    }

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release_device_staging()

void cusbf::detail::FastxPipelineState::release_device_staging ( )

inline

Definition at line 219 of file fastx_pipeline_state.cuh.

                                  {
        thrust::device_vector<char>{}.swap(d_sequence_);
        thrust::device_vector<uint64_t>{}.swap(d_dense_packed_words_);
        for (thrust::device_vector<char>& buffer : d_sequence_pings_) {
            thrust::device_vector<char>{}.swap(buffer);
        }
        thrust::device_vector<uint8_t>{}.swap(d_resultBuffer_);
        thrust::device_vector<QueryLayoutRecord>{}.swap(d_query_layout_records_);
        thrust::device_vector<uint64_t>{}.swap(d_record_positive_kmers_);
    }

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release_host_pings()

void cusbf::detail::FastxPipelineState::release_host_pings ( )

inline

Definition at line 203 of file fastx_pipeline_state.cuh.

                              {
        for (FastxPinnedSequenceBuffer& sequence : normalized_sequence_pings_) {
            sequence.release();
        }
        for (std::vector<NormalizedRecord>& records : normalized_records_pings_) {
            std::vector<NormalizedRecord>{}.swap(records);
        }
    }

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release_host_scratch()

void cusbf::detail::FastxPipelineState::release_host_scratch ( )

inline

Definition at line 212 of file fastx_pipeline_state.cuh.

                                {
        std::string{}.swap(normalized_sequence_scratch_);
        std::vector<NormalizedRecord>{}.swap(normalized_records_scratch_);
        std::vector<uint64_t>{}.swap(record_positive_kmers_scratch_);
        std::vector<uint8_t>{}.swap(result_hits_scratch_);
    }

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result_buffer_device() [1/2]

const thrust::device_vector< uint8_t > & cusbf::detail::FastxPipelineState::result_buffer_device ( ) const

inlinenoexcept

Definition at line 53 of file fastx_pipeline_state.cuh.

                                                                                            {
        return d_resultBuffer_;
    }

result_buffer_device() [2/2]

thrust::device_vector< uint8_t > & cusbf::detail::FastxPipelineState::result_buffer_device ( )

inlinenoexcept

Definition at line 49 of file fastx_pipeline_state.cuh.

                                                                                {
        return d_resultBuffer_;
    }

result_hits_scratch() [1/2]

const std::vector< uint8_t > & cusbf::detail::FastxPipelineState::result_hits_scratch ( ) const

inlinenoexcept

Definition at line 123 of file fastx_pipeline_state.cuh.

                                                                                 {
        return result_hits_scratch_;
    }

result_hits_scratch() [2/2]

std::vector< uint8_t > & cusbf::detail::FastxPipelineState::result_hits_scratch ( )

inlinenoexcept

Definition at line 119 of file fastx_pipeline_state.cuh.

                                                                     {
        return result_hits_scratch_;
    }

sequence_device() [1/2]

const thrust::device_vector< char > & cusbf::detail::FastxPipelineState::sequence_device ( ) const

inlinenoexcept

Definition at line 36 of file fastx_pipeline_state.cuh.

                                                                                    {
        return d_sequence_;
    }

sequence_device() [2/2]

thrust::device_vector< char > & cusbf::detail::FastxPipelineState::sequence_device ( )

inlinenoexcept

Definition at line 32 of file fastx_pipeline_state.cuh.

                                                                        {
        return d_sequence_;
    }

shrink_all()

void cusbf::detail::FastxPipelineState::shrink_all ( )

inline

Definition at line 244 of file fastx_pipeline_state.cuh.

                      {
        release_all();
    }

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shrink_device_staging()

void cusbf::detail::FastxPipelineState::shrink_device_staging ( )

inline

Definition at line 240 of file fastx_pipeline_state.cuh.

                                 {
        release_device_staging();
    }

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shrink_host_scratch()

void cusbf::detail::FastxPipelineState::shrink_host_scratch ( )

inline

Definition at line 236 of file fastx_pipeline_state.cuh.

                               {
        release_host_scratch();
    }

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stage_dense_packed()

Result< void > cusbf::detail::FastxPipelineState::stage_dense_packed ( std::span< const uint64_t >  words, cuda::stream_ref  stream  )

inline

Definition at line 167 of file fastx_pipeline_state.cuh.

                                                                             {
        ensure_dense_packed_capacity(words.size());
        CUSBF_CUDA_TRY(cudaMemcpyAsync(
            thrust::raw_pointer_cast(d_dense_packed_words_.data()),
            words.data(),
            words.size_bytes(),
            cudaMemcpyHostToDevice,
            stream.get()
        ));
        return {};
    }

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stage_sequence()

Result< void > cusbf::detail::FastxPipelineState::stage_sequence ( std::span< const char >  sequence, cuda::stream_ref  stream  )

inline

Definition at line 146 of file fastx_pipeline_state.cuh.

                                                                        {
        ensure_sequence_capacity(sequence.size());
        CUSBF_CUDA_TRY(cudaMemcpyAsync(
            thrust::raw_pointer_cast(d_sequence_.data()),
            sequence.data(),
            sequence.size_bytes(),
            cudaMemcpyHostToDevice,
            stream.get()
        ));
        return {};
    }

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stage_sequence_ping()

Result< device_span< const char > > cusbf::detail::FastxPipelineState::stage_sequence_ping ( size_t  ping, std::string_view  sequence, cuda::stream_ref  stream  )

inline

Definition at line 188 of file fastx_pipeline_state.cuh.

                                                                                     {
        auto& buffer = d_sequence_pings_[ping & 1U];
        if (sequence.size() > buffer.size()) {
            buffer.resize(sequence.size());
        }
        CUSBF_CUDA_TRY(cudaMemcpyAsync(
            thrust::raw_pointer_cast(buffer.data()),
            sequence.data(),
            sequence.size(),
            cudaMemcpyHostToDevice,
            stream.get()
        ));
        return device_span<const char>{thrust::raw_pointer_cast(buffer.data()), sequence.size()};
    }

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staged_dense_packed_view()

Result< device_span< const uint64_t > > cusbf::detail::FastxPipelineState::staged_dense_packed_view ( std::span< const uint64_t >  words, cuda::stream_ref  stream  )

inline

Definition at line 180 of file fastx_pipeline_state.cuh.

                                                                                   {
        CUSBF_TRY(stage_dense_packed(words, stream));
        return device_span<const uint64_t>{
            thrust::raw_pointer_cast(d_dense_packed_words_.data()), words.size()
        };
    }

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staged_sequence_view()

Result< device_span< const char > > cusbf::detail::FastxPipelineState::staged_sequence_view ( std::span< const char >  sequence, cuda::stream_ref  stream  )

inline

Definition at line 159 of file fastx_pipeline_state.cuh.

                                                                              {
        CUSBF_TRY(stage_sequence(sequence, stream));
        return device_span<const char>{
            thrust::raw_pointer_cast(d_sequence_.data()), sequence.size()
        };
    }

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The documentation for this class was generated from the following file:

• fastx_pipeline_state.cuh