alignment_test_utils.h File Reference

#include <nvbio-test/alignment_test_utils.h>
#include <nvbio/basic/timer.h>
#include <nvbio/basic/console.h>
#include <nvbio/basic/cuda/ldg.h>
#include <nvbio/basic/cached_iterator.h>
#include <nvbio/basic/packedstream.h>
#include <nvbio/basic/packedstream_loader.h>
#include <nvbio/basic/vector_view.h>
#include <nvbio/basic/shared_pointer.h>
#include <nvbio/basic/dna.h>
#include <nvbio/alignment/alignment.h>
#include <nvbio/alignment/batched.h>
#include <nvbio/alignment/sink.h>
#include <thrust/device_vector.h>
#include <stdio.h>
#include <stdlib.h>
#include <vector>
#include <algorithm>

Go to the source code of this file.

Classes
struct	nvbio::aln::ScoreMatrices< N, M, aligner_tag >
struct	nvbio::aln::ScoreMatrices< N, M, aln::EditDistanceTag >
struct	nvbio::aln::ScoreMatrices< N, M, aln::SmithWatermanTag >
struct	nvbio::aln::ScoreMatrices< N, M, aln::GotohTag >
struct	nvbio::aln::TestBacktracker

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

Macros
#define	DEBUG_THIS
#define	DEBUG_THIS_STATEMENT(x)   x

Enumerations
enum	nvbio::aln::AlignmentTest {   nvbio::aln::ALL = 0xFFFFFFFFu, nvbio::aln::ED = 1u, nvbio::aln::SW = 2u, nvbio::aln::GOTOH = 4u,   nvbio::aln::ED_BANDED = 8u, nvbio::aln::SW_BANDED = 16u, nvbio::aln::GOTOH_BANDED = 32u, nvbio::aln::SW_WARP = 64u,   nvbio::aln::SW_STRIPED = 128u, nvbio::aln::FUNCTIONAL = 256u }

Functions
vector_view< const char * >	nvbio::aln::make_string (const char *str)
std::string	nvbio::aln::rle (const char *input)
template<uint32 BITS, typename rand_type >
void	nvbio::aln::fill_packed_stream (rand_type &rand, const uint32 value_range, const uint32 n, uint32 *storage)
template<uint32 M, uint32 N, uint32 BAND_LEN, aln::AlignmentType TYPE, typename scheme_type >
int32	nvbio::aln::ref_banded_sw (const uint8 *str, const uint8 *ref, const uint32 pos, const aln::SmithWatermanAligner< TYPE, scheme_type > aligner)
template<uint32 M, uint32 N, uint32 BAND_LEN, aln::AlignmentType TYPE, typename scheme_type >
int32	nvbio::aln::ref_banded_sw (const uint8 *pattern, const uint8 *text, const uint32 pos, const aln::GotohAligner< TYPE, scheme_type > aligner)
template<uint32 M, uint32 N, aln::AlignmentType TYPE, typename scheme_type >
int32	nvbio::aln::ref_sw (const uint8 *str, const uint8 *ref, const aln::SmithWatermanAligner< TYPE, scheme_type > aligner, ScoreMatrices< N, M, aln::SmithWatermanTag > *mat)
template<uint32 M, uint32 N, aln::AlignmentType TYPE>
int32	nvbio::aln::ref_sw (const uint8 *str, const uint8 *ref, const aln::EditDistanceAligner< TYPE > aligner, ScoreMatrices< N, M, aln::EditDistanceTag > *mat)
template<uint32 M, uint32 N, aln::AlignmentType TYPE, typename scheme_type >
int32	nvbio::aln::ref_sw (const uint8 *str, const uint8 *ref, const aln::GotohAligner< TYPE, scheme_type > aligner, ScoreMatrices< N, M, aln::GotohTag > *mat)

Macro Definition Documentation

#define DEBUG_THIS

#define DEBUG_THIS_STATEMENT

(

x)

x