| aligner() const | nvbio::bowtie2::cuda::detail::AlignmentStreamBase< TRACEBACK_STREAM, AlignerType, PipelineType > | inline |
| aligner_type typedef | nvbio::bowtie2::cuda::detail::AlignmentStreamBase< TRACEBACK_STREAM, AlignerType, PipelineType > | |
| AlignmentStreamBase(const PipelineType _pipeline, const aligner_type _aligner, const ParamsPOD _params) | nvbio::bowtie2::cuda::detail::AlignmentStreamBase< TRACEBACK_STREAM, AlignerType, PipelineType > | inline |
| AllTracebackStream(const uint32 _count, const uint32 *_idx, const uint32 _buffer_offset, const uint32 _buffer_size, io::Alignment *_alignments, const uint32 _band_len, const PipelineType _pipeline, const AlignerType _aligner, const ParamsPOD _params) | nvbio::bowtie2::cuda::detail::AllTracebackStream< AlignerType, PipelineType > | inline |
| base_type typedef | nvbio::bowtie2::cuda::detail::AllTracebackStream< AlignerType, PipelineType > | |
| context_type typedef | nvbio::bowtie2::cuda::detail::AllTracebackStream< AlignerType, PipelineType > | |
| finish(const uint32 i, const context_type *context, const uint32 ed, const int32 score) | nvbio::bowtie2::cuda::detail::AllTracebackStream< AlignerType, PipelineType > | inline |
| init_context(const uint32 i, context_type *context) const | nvbio::bowtie2::cuda::detail::AllTracebackStream< AlignerType, PipelineType > | inline |
| load_strings(const uint32 i, const uint32 window_begin, const uint32 window_end, const context_type *context, strings_type *strings) const | nvbio::bowtie2::cuda::detail::AlignmentStreamBase< TRACEBACK_STREAM, AlignerType, PipelineType > | inline |
| m_aligner | nvbio::bowtie2::cuda::detail::AlignmentStreamBase< TRACEBACK_STREAM, AlignerType, PipelineType > | |
| m_alignments | nvbio::bowtie2::cuda::detail::AllTracebackStream< AlignerType, PipelineType > | |
| m_band_len | nvbio::bowtie2::cuda::detail::AllTracebackStream< AlignerType, PipelineType > | |
| m_buffer_offset | nvbio::bowtie2::cuda::detail::AllTracebackStream< AlignerType, PipelineType > | |
| m_buffer_size | nvbio::bowtie2::cuda::detail::AllTracebackStream< AlignerType, PipelineType > | |
| m_count | nvbio::bowtie2::cuda::detail::AllTracebackStream< AlignerType, PipelineType > | |
| m_idx | nvbio::bowtie2::cuda::detail::AllTracebackStream< AlignerType, PipelineType > | |
| m_mate_type | nvbio::bowtie2::cuda::detail::AllTracebackStream< AlignerType, PipelineType > | |
| m_params | nvbio::bowtie2::cuda::detail::AlignmentStreamBase< TRACEBACK_STREAM, AlignerType, PipelineType > | |
| m_pipeline | nvbio::bowtie2::cuda::detail::AlignmentStreamBase< TRACEBACK_STREAM, AlignerType, PipelineType > | |
| mate_type() const | nvbio::bowtie2::cuda::detail::AllTracebackStream< AlignerType, PipelineType > | inline |
| max_pattern_length() const | nvbio::bowtie2::cuda::detail::AllTracebackStream< AlignerType, PipelineType > | inline |
| max_text_length() const | nvbio::bowtie2::cuda::detail::AllTracebackStream< AlignerType, PipelineType > | inline |
| output(const uint32 i, const context_type *context) | nvbio::bowtie2::cuda::detail::AllTracebackStream< AlignerType, PipelineType > | inline |
| pattern_length(const uint32 i, const context_type *context) const | nvbio::bowtie2::cuda::detail::AlignmentStreamBase< TRACEBACK_STREAM, AlignerType, PipelineType > | inline |
| scheme_type typedef | nvbio::bowtie2::cuda::detail::AllTracebackStream< AlignerType, PipelineType > | |
| size() const | nvbio::bowtie2::cuda::detail::AllTracebackStream< AlignerType, PipelineType > | inline |
| strings_type typedef | nvbio::bowtie2::cuda::detail::AlignmentStreamBase< TRACEBACK_STREAM, AlignerType, PipelineType > | |
| text_length(const uint32 i, const context_type *context) const | nvbio::bowtie2::cuda::detail::AlignmentStreamBase< TRACEBACK_STREAM, AlignerType, PipelineType > | inline |
1.8.4