aligner() const | nvbio::bowtie2::cuda::detail::AlignmentStreamBase< SCORE_STREAM, AlignerType, PipelineType > | inline |
aligner_type typedef | nvbio::bowtie2::cuda::detail::AlignmentStreamBase< SCORE_STREAM, AlignerType, PipelineType > | |
AlignmentStreamBase(const PipelineType _pipeline, const aligner_type _aligner, const ParamsPOD _params) | nvbio::bowtie2::cuda::detail::AlignmentStreamBase< SCORE_STREAM, AlignerType, PipelineType > | inline |
base_type typedef | nvbio::bowtie2::cuda::detail::BestAnchorScoreStream< AlignerType, PipelineType > | |
BestAnchorScoreStream(const uint32 _band_len, const PipelineType _pipeline, const AlignerType _aligner, const ParamsPOD _params) | nvbio::bowtie2::cuda::detail::BestAnchorScoreStream< AlignerType, PipelineType > | inline |
context_type typedef | nvbio::bowtie2::cuda::detail::BestAnchorScoreStream< AlignerType, PipelineType > | |
init_context(const uint32 i, context_type *context) const | nvbio::bowtie2::cuda::detail::BestAnchorScoreStream< 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< SCORE_STREAM, AlignerType, PipelineType > | inline |
m_aligner | nvbio::bowtie2::cuda::detail::AlignmentStreamBase< SCORE_STREAM, AlignerType, PipelineType > | |
m_band_len | nvbio::bowtie2::cuda::detail::BestAnchorScoreStream< AlignerType, PipelineType > | |
m_params | nvbio::bowtie2::cuda::detail::AlignmentStreamBase< SCORE_STREAM, AlignerType, PipelineType > | |
m_pipeline | nvbio::bowtie2::cuda::detail::AlignmentStreamBase< SCORE_STREAM, AlignerType, PipelineType > | |
max_pattern_length() const | nvbio::bowtie2::cuda::detail::BestAnchorScoreStream< AlignerType, PipelineType > | inline |
max_text_length() const | nvbio::bowtie2::cuda::detail::BestAnchorScoreStream< AlignerType, PipelineType > | inline |
output(const uint32 i, const context_type *context) const | nvbio::bowtie2::cuda::detail::BestAnchorScoreStream< AlignerType, PipelineType > | inline |
pattern_length(const uint32 i, const context_type *context) const | nvbio::bowtie2::cuda::detail::AlignmentStreamBase< SCORE_STREAM, AlignerType, PipelineType > | inline |
scheme_type typedef | nvbio::bowtie2::cuda::detail::BestAnchorScoreStream< AlignerType, PipelineType > | |
size() const | nvbio::bowtie2::cuda::detail::BestAnchorScoreStream< AlignerType, PipelineType > | inline |
strings_type typedef | nvbio::bowtie2::cuda::detail::AlignmentStreamBase< SCORE_STREAM, AlignerType, PipelineType > | |
text_length(const uint32 i, const context_type *context) const | nvbio::bowtie2::cuda::detail::AlignmentStreamBase< SCORE_STREAM, AlignerType, PipelineType > | inline |