assembly_types.h File Reference

#include <nvbio/basic/types.h>
#include <nvbio/basic/vector.h>
#include <nvbio/basic/packed_vector.h>
#include <nvbio/strings/string_set.h>
#include <nvbio/strings/infix.h>
#include <nvbio/io/sequence/sequence.h>
#include <nvbio/io/sequence/sequence_access.h>
#include <nvbio/basic/dna.h>

Go to the source code of this file.

Classes
struct	cigar_op

Macros
#define	DNA_SYMBOL_BITS   2U
#define	DNA_SYMBOL_MASK   ((1u << DNA_SYMBOL_BITS) - 1u)

Typedefs
typedef nvbio::vector < device_tag, uint8 >	D_VectorU8
typedef nvbio::vector < host_tag, uint8 >	H_VectorU8
typedef nvbio::vector < device_tag, uint16 >	D_VectorU16
typedef nvbio::vector < host_tag, uint16 >	H_VectorU16
typedef nvbio::vector < device_tag, uint32 >	D_VectorU32
typedef nvbio::vector < host_tag, uint32 >	H_VectorU32
typedef nvbio::vector < device_tag, uint64 >	D_VectorU64
typedef nvbio::vector < host_tag, uint64 >	H_VectorU64
typedef nvbio::vector < device_tag, int32 >	D_VectorI32
typedef nvbio::vector < host_tag, int32 >	H_VectorI32
typedef nvbio::vector < device_tag, ulonglong2 >	D_VectorU64_2
typedef nvbio::vector < host_tag, ulonglong2 >	H_VectorU64_2
typedef nvbio::PackedVector < host_tag, 2, false, uint64 >	H_VectorDNA
typedef nvbio::PackedVector < device_tag, 2, false, uint64 >	D_VectorDNA
typedef H_VectorDNA::stream_type	H_StreamDNA
typedef H_VectorDNA::const_stream_type	H_ConstStreamDNA
typedef D_VectorDNA::stream_type	D_StreamDNA
typedef D_VectorDNA::const_stream_type	D_ConstStreamDNA
typedef ConcatenatedStringSet < H_StreamDNA, uint64 * >	H_SequenceSet
typedef ConcatenatedStringSet < D_StreamDNA, uint64 * >	D_SequenceSet
typedef string_set_infix_coord_type	SequenceSetKmerCoord
typedef nvbio::vector < host_tag, SequenceSetKmerCoord >	H_VectorSetKmerCoord
typedef nvbio::vector < device_tag, SequenceSetKmerCoord >	D_VectorSetKmerCoord
typedef nvbio::vector < host_tag, SequenceSetKmerCoord * > ::iterator	H_KmerIterator
typedef nvbio::vector < device_tag, SequenceSetKmerCoord * > ::iterator	D_KmerIterator
typedef nvbio::io::SequenceDataAccess < DNA > ::sequence_string_set_type	RefSequenceSet
typedef const ulong2 *	ranges_iterator
typedef nvbio::SparseStringSet < H_VectorDNA, ranges_iterator >	H_RefRangesSet
typedef nvbio::SparseStringSet < D_VectorDNA, ranges_iterator >	D_RefRangesSet
typedef nvbio::PackedVector < host_tag, 4, false, uint64 >	H_VectorDNA16
typedef nvbio::PackedVector < device_tag, 4, false, uint64 >	D_VectorDNA16
typedef nvbio::vector < device_tag, cigar_op >	D_VectorCigarOp
typedef nvbio::vector < host_tag, cigar_op >	H_VectorCigarOp

Macro Definition Documentation

#define DNA_SYMBOL_BITS   2U

Definition at line 41 of file assembly_types.h.

#define DNA_SYMBOL_MASK   ((1u << DNA_SYMBOL_BITS) - 1u)

Definition at line 42 of file assembly_types.h.

Typedef Documentation

typedef D_VectorDNA::const_stream_type D_ConstStreamDNA

Definition at line 62 of file assembly_types.h.

typedef nvbio::vector<device_tag, SequenceSetKmerCoord*>::iterator D_KmerIterator

Definition at line 71 of file assembly_types.h.

typedef nvbio::SparseStringSet<D_VectorDNA, ranges_iterator> D_RefRangesSet

Definition at line 77 of file assembly_types.h.

typedef ConcatenatedStringSet<D_StreamDNA, uint64*> D_SequenceSet

Definition at line 65 of file assembly_types.h.

typedef D_VectorDNA::stream_type D_StreamDNA

Definition at line 61 of file assembly_types.h.

typedef nvbio::vector<device_tag, cigar_op> D_VectorCigarOp

Definition at line 114 of file assembly_types.h.

typedef nvbio::PackedVector<device_tag, 2, false, uint64> D_VectorDNA

Definition at line 58 of file assembly_types.h.

typedef nvbio::PackedVector<device_tag, 4, false, uint64> D_VectorDNA16

Definition at line 82 of file assembly_types.h.

typedef nvbio::vector<device_tag, int32> D_VectorI32

Definition at line 52 of file assembly_types.h.

typedef nvbio::vector<device_tag, SequenceSetKmerCoord> D_VectorSetKmerCoord

Definition at line 68 of file assembly_types.h.

typedef nvbio::vector<device_tag, uint16> D_VectorU16

Definition at line 46 of file assembly_types.h.

typedef nvbio::vector<device_tag, uint32> D_VectorU32

Definition at line 48 of file assembly_types.h.

typedef nvbio::vector<device_tag, uint64> D_VectorU64

Definition at line 50 of file assembly_types.h.

typedef nvbio::vector<device_tag, ulonglong2> D_VectorU64_2

Definition at line 54 of file assembly_types.h.

typedef nvbio::vector<device_tag, uint8> D_VectorU8

Definition at line 44 of file assembly_types.h.

typedef H_VectorDNA::const_stream_type H_ConstStreamDNA

Definition at line 60 of file assembly_types.h.

typedef nvbio::vector<host_tag, SequenceSetKmerCoord*>::iterator H_KmerIterator

Definition at line 70 of file assembly_types.h.

typedef nvbio::SparseStringSet<H_VectorDNA, ranges_iterator> H_RefRangesSet

Definition at line 76 of file assembly_types.h.

typedef ConcatenatedStringSet<H_StreamDNA, uint64*> H_SequenceSet

Definition at line 64 of file assembly_types.h.

typedef H_VectorDNA::stream_type H_StreamDNA

Definition at line 59 of file assembly_types.h.

typedef nvbio::vector<host_tag, cigar_op> H_VectorCigarOp

Definition at line 115 of file assembly_types.h.

typedef nvbio::PackedVector<host_tag, 2, false, uint64> H_VectorDNA

Definition at line 57 of file assembly_types.h.

typedef nvbio::PackedVector<host_tag, 4, false, uint64> H_VectorDNA16

Definition at line 81 of file assembly_types.h.

typedef nvbio::vector<host_tag, int32> H_VectorI32

Definition at line 53 of file assembly_types.h.

typedef nvbio::vector<host_tag, SequenceSetKmerCoord> H_VectorSetKmerCoord

Definition at line 67 of file assembly_types.h.

typedef nvbio::vector<host_tag, uint16> H_VectorU16

Definition at line 47 of file assembly_types.h.

typedef nvbio::vector<host_tag, uint32> H_VectorU32

Definition at line 49 of file assembly_types.h.

typedef nvbio::vector<host_tag, uint64> H_VectorU64

Definition at line 51 of file assembly_types.h.

typedef nvbio::vector<host_tag, ulonglong2> H_VectorU64_2

Definition at line 55 of file assembly_types.h.

typedef nvbio::vector<host_tag, uint8> H_VectorU8

Definition at line 45 of file assembly_types.h.

typedef const ulong2* ranges_iterator

Definition at line 75 of file assembly_types.h.

typedef nvbio::io::SequenceDataAccess<DNA>::sequence_string_set_type RefSequenceSet

Definition at line 73 of file assembly_types.h.

typedef string_set_infix_coord_type SequenceSetKmerCoord

Definition at line 66 of file assembly_types.h.