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)