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Classes | Functions
Utilities
Alignment Module

Detailed Description

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
 

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)
 

Function Documentation

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 
)

Calculate the maximum possible number of pattern gaps that could occur in a given score boundary

Definition at line 70 of file utils_inl.h.

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 
)

Calculate the maximum possible number of pattern gaps that could occur in a given score boundary

Definition at line 98 of file utils_inl.h.

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 
)

Calculate the maximum possible number of pattern gaps that could occur in a given score boundary

Definition at line 152 of file utils_inl.h.

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 
)

Calculate the maximum possible number of pattern gaps that could occur in a given score boundary

Definition at line 42 of file utils_inl.h.

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 
)

Calculate the maximum possible number of reference gaps that could occur in a given score boundary

Definition at line 84 of file utils_inl.h.

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 
)

Calculate the maximum possible number of reference gaps that could occur in a given score boundary

Definition at line 125 of file utils_inl.h.

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 
)

Calculate the maximum possible number of reference gaps that could occur in a given score boundary

Definition at line 182 of file utils_inl.h.

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 
)

Calculate the maximum possible number of reference gaps that could occur in a given score boundary

Definition at line 56 of file utils_inl.h.

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