sw_inl.h File Reference

#include <nvbio/basic/packedstream.h>
#include <nvbio/alignment/sink.h>
#include <nvbio/alignment/utils.h>
#include <nvbio/alignment/alignment_base_inl.h>
#include <nvbio/basic/iterator.h>

Go to the source code of this file.

Classes
struct	nvbio::aln::priv::SWScoringContext< BAND_LEN, TYPE, algorithm_tag >
struct	nvbio::aln::priv::SWCheckpointedScoringContext< BAND_LEN, TYPE, algorithm_tag, checkpoint_type >
struct	nvbio::aln::priv::SWCheckpointContext< BAND_LEN, TYPE, CHECKPOINTS, checkpoint_type >
struct	nvbio::aln::priv::SWSubmatrixContext< BAND_LEN, TYPE, CHECKPOINTS, checkpoint_type, submatrix_type >
struct	nvbio::aln::priv::sw_alignment_score_dispatch< BAND_LEN, TYPE, algorithm_tag, symbol_type >
struct	nvbio::aln::priv::sw_alignment_score_dispatch< BAND_LEN, TYPE, PatternBlockingTag, symbol_type >
struct	nvbio::aln::priv::sw_alignment_score_dispatch< BAND_LEN, TYPE, TextBlockingTag, symbol_type >
struct	nvbio::aln::priv::sw_bandlen_selector< TYPE, DIM, symbol_type >
struct	nvbio::aln::priv::sw_bandlen_selector< TYPE, DIM, simd4u8 >
struct	nvbio::aln::priv::alignment_score_dispatch< SmithWatermanAligner< TYPE, scoring_type, algorithm_tag >, pattern_string, qual_string, text_string, column_type >
struct	nvbio::aln::priv::alignment_checkpointed_dispatch< CHECKPOINTS, SmithWatermanAligner< TYPE, scoring_type >, pattern_string, qual_string, text_string, column_type >

Namespaces
	nvbio
	Define a vector_view POD type and plain_view() for std::vector.
	nvbio::aln
	nvbio::aln::priv

Functions
template<uint32 CHECKPOINTS, AlignmentType TYPE, typename scoring_type , typename checkpoint_type , typename submatrix_type , typename output_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	nvbio::aln::priv::alignment_traceback (const SmithWatermanAligner< TYPE, scoring_type > aligner, checkpoint_type checkpoints, const uint32 checkpoint_id, submatrix_type submatrix, const uint32 submatrix_width, const uint32 submatrix_height, uint8 &state, uint2 &sink, output_type &output)