NVBIO
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A scoring stream, fetching the input hits to score from the hit queue indexed by the input sorting order, and assigning them their score and sink attributes.
Definition at line 54 of file score_all_inl.h.
#include <score_all_inl.h>
Public Types | |
typedef AlignmentStreamBase < SCORE_STREAM, AlignerType, PipelineType > | base_type |
typedef base_type::context_type | context_type |
typedef base_type::scheme_type | scheme_type |
Public Types inherited from nvbio::bowtie2::cuda::detail::AlignmentStreamBase< SCORE_STREAM, AlignerType, PipelineType > | |
typedef AlignmentStrings < AlignerType, PipelineType > | strings_type |
typedef PipelineType::scheme_type | scheme_type |
typedef AlignerType | aligner_type |
Public Members | |
const uint32 | m_band_len |
const uint32 | m_buffer_offset |
const uint32 | m_buffer_size |
uint32 * | m_counter |
Public Members inherited from nvbio::bowtie2::cuda::detail::AlignmentStreamBase< SCORE_STREAM, AlignerType, PipelineType > | |
PipelineType | m_pipeline |
the pipeline object More... | |
aligner_type | m_aligner |
the aligner More... | |
ParamsPOD | m_params |
global parameters More... | |
typedef AlignmentStreamBase<SCORE_STREAM,AlignerType,PipelineType> nvbio::bowtie2::cuda::detail::AllScoreStream< AlignerType, PipelineType >::base_type |
Definition at line 56 of file score_all_inl.h.
typedef base_type::context_type nvbio::bowtie2::cuda::detail::AllScoreStream< AlignerType, PipelineType >::context_type |
Definition at line 57 of file score_all_inl.h.
typedef base_type::scheme_type nvbio::bowtie2::cuda::detail::AllScoreStream< AlignerType, PipelineType >::scheme_type |
Definition at line 58 of file score_all_inl.h.
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constructor
_band_len | effective band length; NOTE: this value must match the template BAND_LEN parameter used for instantiating aln::BatchedBandedAlignmentScore. |
_pipeline | the pipeline object |
_aligner | the aligner object |
Definition at line 70 of file score_all_inl.h.
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initialize the i-th context
Definition at line 101 of file score_all_inl.h.
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return the maximum pattern length
Definition at line 86 of file score_all_inl.h.
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return the maximum text length
Definition at line 91 of file score_all_inl.h.
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handle the output
Definition at line 134 of file score_all_inl.h.
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return the stream size
Definition at line 96 of file score_all_inl.h.
const uint32 nvbio::bowtie2::cuda::detail::AllScoreStream< AlignerType, PipelineType >::m_band_len |
Definition at line 158 of file score_all_inl.h.
const uint32 nvbio::bowtie2::cuda::detail::AllScoreStream< AlignerType, PipelineType >::m_buffer_offset |
Definition at line 159 of file score_all_inl.h.
const uint32 nvbio::bowtie2::cuda::detail::AllScoreStream< AlignerType, PipelineType >::m_buffer_size |
Definition at line 160 of file score_all_inl.h.
uint32* nvbio::bowtie2::cuda::detail::AllScoreStream< AlignerType, PipelineType >::m_counter |
Definition at line 161 of file score_all_inl.h.