alignment.h File Reference

#include <nvbio/basic/types.h>
#include <nvbio/alignment/alignment_base.h>
#include <nvbio/alignment/alignment_inl.h>
#include <nvbio/alignment/banded_inl.h>
#include <nvbio/alignment/utils.h>

Go to the source code of this file.

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 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 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 , typename sink_type >
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 qual_string , typename text_string , typename sink_type >
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, 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<typename aligner_type , typename pattern_string , typename qual_string , typename text_string , typename sink_type , typename column_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	nvbio::aln::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, column_type column)
template<uint32 MAX_TEXT_LEN, typename aligner_type , typename pattern_string , typename qual_string , typename text_string , typename sink_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	nvbio::aln::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 CHECKPOINTS, typename aligner_type , typename pattern_string , typename qual_string , typename text_string , typename backtracer_type , typename checkpoints_type , typename submatrix_type , typename column_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE Alignment < int32 >	nvbio::aln::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, column_type column)
template<uint32 MAX_PATTERN_LEN, uint32 MAX_TEXT_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::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)