banded_inl.h File Reference

#include <nvbio/basic/types.h>
#include <nvbio/alignment/utils.h>
#include <nvbio/alignment/alignment_base_inl.h>
#include <nvbio/alignment/ed/ed_banded_inl.h>
#include <nvbio/alignment/sw/sw_banded_inl.h>
#include <nvbio/alignment/gotoh/gotoh_banded_inl.h>
#include <nvbio/alignment/myers/myers_banded_inl.h>

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

Functions
template<uint32 BAND_LEN, typename aligner_type , typename pattern_string , typename qual_string , typename text_string , typename sink_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	nvbio::aln::banded_alignment_score (const aligner_type aligner, const pattern_string pattern, const qual_string quals, const text_string text, const int32 min_score, sink_type &sink)
template<uint32 BAND_LEN, typename aligner_type , typename pattern_string , typename text_string , typename sink_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	nvbio::aln::banded_alignment_score (const aligner_type aligner, const pattern_string pattern, const text_string text, const int32 min_score, sink_type &sink)
template<uint32 BAND_LEN, typename aligner_type , typename pattern_string , typename qual_string , typename text_string >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32	nvbio::aln::banded_alignment_score (const aligner_type aligner, const pattern_string pattern, const qual_string quals, const text_string text, const int32 min_score)
template<uint32 BAND_LEN, typename aligner_type , typename pattern_string , typename text_string >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32	nvbio::aln::banded_alignment_score (const aligner_type aligner, const pattern_string pattern, const text_string text, const int32 min_score)
template<uint32 BAND_LEN, typename aligner_type , typename pattern_string , typename qual_string , typename text_string , typename sink_type , typename checkpoint_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	nvbio::aln::banded_alignment_score (const aligner_type aligner, const pattern_string pattern, const qual_string quals, const text_string 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, typename aligner_type , typename pattern_string , typename qual_string , typename text_string , typename sink_type , typename checkpoint_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	nvbio::aln::banded_alignment_score_checkpoints (const aligner_type aligner, const pattern_string pattern, const qual_string quals, const text_string text, const int32 min_score, sink_type &sink, checkpoint_type checkpoints)
template<uint32 BAND_LEN, uint32 CHECKPOINTS, typename aligner_type , typename pattern_string , typename qual_string , typename text_string , typename checkpoint_type , typename submatrix_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	nvbio::aln::banded_alignment_score_submatrix (const aligner_type aligner, const pattern_string pattern, const qual_string quals, const text_string text, const int32 min_score, checkpoint_type checkpoints, const uint32 checkpoint_id, submatrix_type submatrix)
template<uint32 BAND_LEN, uint32 CHECKPOINTS, typename aligner_type , typename pattern_string , typename qual_string , typename text_string , typename backtracer_type , typename checkpoints_type , typename submatrix_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE Alignment < int32 >	nvbio::aln::banded_alignment_traceback (const aligner_type aligner, const pattern_string pattern, const qual_string quals, const text_string text, const int32 min_score, backtracer_type &backtracer, checkpoints_type checkpoints, submatrix_type submatrix)
template<uint32 BAND_LEN, uint32 MAX_PATTERN_LEN, uint32 CHECKPOINTS, typename aligner_type , typename pattern_string , typename qual_string , typename text_string , typename backtracer_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE Alignment < int32 >	nvbio::aln::banded_alignment_traceback (const aligner_type aligner, const pattern_string pattern, const qual_string quals, const text_string text, const int32 min_score, backtracer_type &backtracer)