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sw_warp_inl.h File Reference
#include <nvbio/basic/cuda/arch.h>
#include <nvbio/basic/cuda/scan.h>
#include <nvbio/alignment/sink.h>
#include <nvbio/alignment/utils.h>
#include <nvbio/alignment/warp_utils.h>
#include <nvbio/alignment/alignment_base_inl.h>

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Namespaces

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

Functions

template<uint32 BLOCKDIM, AlignmentType TYPE, typename scoring_type , typename string_type , typename qual_type , typename ref_type , typename column_type >
NVBIO_FORCEINLINE NVBIO_DEVICE
int32 
nvbio::aln::priv::sw_alignment_score (const scoring_type &scoring, string_type str, qual_type quals, ref_type ref, const int32 min_score, uint2 *sink, column_type temp)
 
template<uint32 BLOCKDIM, AlignmentType TYPE, typename scoring_type , typename pattern_string , typename qual_string , typename text_string , typename column_type >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE int32 
nvbio::aln::priv::alignment_score (const SmithWatermanAligner< TYPE, scoring_type > aligner, const pattern_string pattern, const qual_string quals, const text_string text, const int32 min_score, uint2 *sink, column_type column)