utils.h File Reference

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

Go to the source code of this file.

Classes
struct	nvbio::aln::checkpoint_storage_type< aligner_type >
struct	nvbio::aln::checkpoint_storage_type< EditDistanceAligner< TYPE, algorithm_tag > >
struct	nvbio::aln::checkpoint_storage_type< HammingDistanceAligner< TYPE, scoring_type, algorithm_tag > >
struct	nvbio::aln::checkpoint_storage_type< SmithWatermanAligner< TYPE, scoring_type, algorithm_tag > >
struct	nvbio::aln::checkpoint_storage_type< GotohAligner< TYPE, scoring_type, algorithm_tag > >
struct	nvbio::aln::column_storage_type< aligner_type >
struct	nvbio::aln::column_storage_type< EditDistanceAligner< TYPE, algorithm_tag > >
struct	nvbio::aln::column_storage_type< HammingDistanceAligner< TYPE, scoring_type, algorithm_tag > >
struct	nvbio::aln::column_storage_type< SmithWatermanAligner< TYPE, scoring_type, algorithm_tag > >
struct	nvbio::aln::column_storage_type< GotohAligner< TYPE, scoring_type, algorithm_tag > >
struct	nvbio::aln::direction_vector_traits< aligner_type >
struct	nvbio::aln::direction_vector_traits< GotohAligner< TYPE, scoring_type, algorithm_tag > >
struct	nvbio::aln::SimpleSmithWatermanScheme
struct	nvbio::aln::SimpleGotohScheme
struct	nvbio::aln::trivial_quality_string
struct	nvbio::aln::trivial_quality_string_set

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

Functions
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<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)