myers_banded_inl.h File Reference

#include <nvbio/basic/types.h>
#include <nvbio/basic/numbers.h>

Go to the source code of this file.

Classes
struct	nvbio::aln::priv::MyersBitVectors< ALPHABET_SIZE >
struct	nvbio::aln::priv::MyersBitVectors< 2 >
struct	nvbio::aln::priv::MyersBitVectors< 4 >
struct	nvbio::aln::priv::MyersBitVectors< 5 >

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

Functions
template<uint32 BAND_WIDTH>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int	nvbio::aln::priv::diagonal_column (const uint32 B_c_ref, uint32 &VP, uint32 &VN)
template<uint32 BAND_WIDTH>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int	nvbio::aln::priv::horizontal_column (const uint32 B_c_ref, uint32 &VP, uint32 &VN, const int s)
template<uint32 BAND_WIDTH, uint32 C, AlignmentType TYPE, uint32 ALPHABET_SIZE, typename pattern_string , typename text_string , typename sink_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	nvbio::aln::priv::banded_myers (const pattern_string pattern, const text_string text, const int16 min_score, sink_type &sink)
template<uint32 BAND_LEN, AlignmentType TYPE, uint32 ALPHABET_SIZE, typename pattern_type , typename qual_type , typename text_type , typename sink_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	nvbio::aln::priv::banded_alignment_score (const EditDistanceAligner< TYPE, MyersTag< ALPHABET_SIZE > > &aligner, pattern_type pattern, qual_type quals, text_type text, const int32 min_score, sink_type &sink)
template<uint32 BAND_LEN, AlignmentType TYPE, uint32 ALPHABET_SIZE, typename pattern_type , typename qual_type , typename text_type , typename sink_type , typename checkpoint_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	nvbio::aln::priv::banded_alignment_score (const EditDistanceAligner< TYPE, MyersTag< ALPHABET_SIZE > > &aligner, pattern_type pattern, qual_type quals, text_type text, const int32 min_score, const uint32 window_begin, const uint32 window_end, sink_type &sink, checkpoint_type checkpoint)