nvbio::bowtie2::cuda::detail::seed_mapper< CASE_PRUNING_MAPPING > Struct Template Reference

Detailed description

template<>
struct nvbio::bowtie2::cuda::detail::seed_mapper< CASE_PRUNING_MAPPING >

perform approximate seed-mapping allowing 1 mismatch using case-pruning, i.e:

• split the seed in two,
• perform exact mapping of the first half and allow 1 mismatch in the second half
• perform exact mapping of the second half and allow 1 mismatch in the first half

Definition at line 373 of file mapping_inl.h.

#include <mapping_inl.h>

Static Public Methods
template<typename SeedIterator , typename FMType , typename rFMType , typename HitType >
NVBIO_FORCEINLINE static NVBIO_DEVICE void	enact (const FMType fmi, const rFMType rfmi, const SeedIterator seed, const uint2 read_range, const uint32 pos, const uint32 seed_len, HitType &hitheap, uint32 &range_sum, uint32 &range_count, const ParamsPOD &params, const bool fw, const bool rc)

Member Function Documentation

template<typename SeedIterator , typename FMType , typename rFMType , typename HitType >

NVBIO_FORCEINLINE static NVBIO_DEVICE void nvbio::bowtie2::cuda::detail::seed_mapper< CASE_PRUNING_MAPPING >::enact ( const FMType  fmi, const rFMType  rfmi, const SeedIterator  seed, const uint2  read_range, const uint32  pos, const uint32  seed_len, HitType &  hitheap, uint32 &  range_sum, uint32 &  range_count, const ParamsPOD &  params, const bool  fw, const bool  rc  )

inlinestatic

Definition at line 377 of file mapping_inl.h.

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The documentation for this struct was generated from the following file:

• E:/git/nvbio/nvBowtie/bowtie2/cuda/mapping_inl.h