ed_banded_inl.h File Reference

#include <nvbio/basic/types.h>
#include <nvbio/basic/numbers.h>
#include <nvbio/alignment/sw/sw_banded_inl.h>
#include <nvbio/alignment/ed/ed_utils.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 BAND_LEN, AlignmentType TYPE, typename pattern_type , typename qual_type , typename text_type , typename sink_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	nvbio::aln::priv::banded_alignment_score (const EditDistanceAligner< TYPE > &aligner, pattern_type pattern, qual_type quals, text_type text, const int32 min_score, sink_type &sink)
template<uint32 BAND_LEN, AlignmentType TYPE, typename pattern_type , typename qual_type , typename text_type , typename sink_type , typename checkpoint_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	nvbio::aln::priv::banded_alignment_score (const EditDistanceAligner< TYPE > &aligner, pattern_type pattern, qual_type quals, text_type text, const int32 min_score, const uint32 window_begin, const uint32 window_end, sink_type &sink, checkpoint_type checkpoint)
template<uint32 BAND_LEN, uint32 CHECKPOINTS, AlignmentType TYPE, typename pattern_type , typename qual_type , typename text_type , typename sink_type , typename checkpoint_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	nvbio::aln::priv::banded_alignment_checkpoints (const EditDistanceAligner< TYPE > &aligner, pattern_type pattern, qual_type quals, text_type text, const int32 min_score, sink_type &sink, checkpoint_type checkpoints)
template<uint32 BAND_LEN, uint32 CHECKPOINTS, AlignmentType TYPE, typename pattern_string , typename qual_string , typename text_string , typename checkpoint_type , typename submatrix_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	nvbio::aln::priv::banded_alignment_submatrix (const EditDistanceAligner< TYPE > &aligner, pattern_string pattern, qual_string quals, text_string text, const int32 min_score, checkpoint_type checkpoints, const uint32 checkpoint_id, submatrix_type submatrix)
template<uint32 BAND_LEN, uint32 CHECKPOINTS, AlignmentType TYPE, typename checkpoint_type , typename submatrix_type , typename backtracer_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	nvbio::aln::priv::banded_alignment_traceback (const EditDistanceAligner< TYPE > &aligner, checkpoint_type checkpoints, const uint32 checkpoint_id, submatrix_type submatrix, const uint32 submatrix_height, uint8 &state, uint2 &sink, backtracer_type &backtracer)