utils_inl.h File Reference

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

Go to the source code of this file.

Classes
struct	nvbio::aln::select_dispatch< BAND_LEN, score_type >
struct	nvbio::aln::select_dispatch< BAND_LEN, simd4u8 >

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

Functions
template<AlignmentType TYPE, typename algorithm_tag >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	nvbio::aln::max_pattern_gaps (const EditDistanceAligner< TYPE, algorithm_tag > &aligner, int32 min_score, int32 pattern_len)
template<AlignmentType TYPE, typename algorithm_tag >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	nvbio::aln::max_text_gaps (const EditDistanceAligner< TYPE, algorithm_tag > &aligner, int32 min_score, int32 pattern_len)
template<AlignmentType TYPE, typename scoring_scheme_type , typename algorithm_tag >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	nvbio::aln::max_pattern_gaps (const HammingDistanceAligner< TYPE, scoring_scheme_type, algorithm_tag > &aligner, int32 min_score, int32 pattern_len)
template<AlignmentType TYPE, typename scoring_scheme_type , typename algorithm_tag >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	nvbio::aln::max_text_gaps (const HammingDistanceAligner< TYPE, scoring_scheme_type, algorithm_tag > &aligner, int32 min_score, int32 pattern_len)
template<AlignmentType TYPE, typename scoring_scheme_type , typename algorithm_tag >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	nvbio::aln::max_pattern_gaps (const SmithWatermanAligner< TYPE, scoring_scheme_type, algorithm_tag > &aligner, int32 min_score, int32 pattern_len)
template<AlignmentType TYPE, typename scoring_scheme_type , typename algorithm_tag >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	nvbio::aln::max_text_gaps (const SmithWatermanAligner< TYPE, scoring_scheme_type, algorithm_tag > &aligner, int32 min_score, int32 pattern_len)
template<AlignmentType TYPE, typename scoring_scheme_type , typename algorithm_tag >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	nvbio::aln::max_pattern_gaps (const GotohAligner< TYPE, scoring_scheme_type, algorithm_tag > &aligner, int32 min_score, int32 pattern_len)
template<AlignmentType TYPE, typename scoring_scheme_type , typename algorithm_tag >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	nvbio::aln::max_text_gaps (const GotohAligner< TYPE, scoring_scheme_type, algorithm_tag > &aligner, int32 min_score, int32 pattern_len)
template<uint32 BAND_LEN>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	nvbio::aln::save_Mth (const uint4 M, const simd4u8 *band, simd4u8 &best_score)
template<uint32 BAND_LEN, typename sink_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	nvbio::aln::save_Mth (const uint4 M, const simd4u8 *band, const uint32 i, sink_type &sink, const simd4u8 mask)
template<uint32 BAND_LEN, typename score_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	nvbio::aln::save_Mth (const uint32 M, const score_type *band, score_type &best_score)
template<uint32 BAND_LEN, typename score_type , typename sink_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	nvbio::aln::save_Mth (const uint32 M, const score_type *band, const uint32 i, sink_type &sink)
template<uint32 BAND_LEN, typename score_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	nvbio::aln::save_boundary (const uint32 block, const uint32 M, const score_type *band, score_type &best_score)
template<uint32 BAND_LEN, typename score_type , typename sink_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	nvbio::aln::save_boundary (const uint32 block, const uint32 M, const score_type *band, const uint32 i, sink_type &sink)
template<uint32 BAND_LEN, typename sink_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	nvbio::aln::save_boundary (const uint32 block, const uint4 M, const simd4u8 *band, const uint32 i, sink_type &sink, const simd4u8 active_mask)