BamTools Namespace Reference

Classes
struct	BamAlignment
struct	CigarOp
struct	RefEdit
struct	RefData
struct	Chunk
struct	ReferenceIndex
class	BamReader
class	BamWriter
struct	BgzfThread
struct	BgzfData

Typedefs
typedef std::vector< RefData >	RefVector
typedef std::vector< BamAlignment >	BamAlignmentVector
typedef std::vector< Chunk >	ChunkVector
typedef std::map< uint32_t, ChunkVector >	BamBinMap
typedef std::vector< uint64_t >	LinearOffsetVector
typedef std::vector < ReferenceIndex >	BamIndex

Functions
bool	ChunkLessThan (const Chunk &lhs, const Chunk &rhs)

Variables
const int	BAM_CORE_SIZE = 32
const int	BAM_CMATCH = 0
const int	BAM_CINS = 1
const int	BAM_CDEL = 2
const int	BAM_CREF_SKIP = 3
const int	BAM_CSOFT_CLIP = 4
const int	BAM_CHARD_CLIP = 5
const int	BAM_CPAD = 6
const int	BAM_CIGAR_SHIFT = 4
const int	BAM_CIGAR_MASK = ((1 << BAM_CIGAR_SHIFT) - 1)
const int	MAX_BIN = 37450
const int	BAM_MIN_CHUNK_GAP = 32768
const int	BAM_LIDX_SHIFT = 14
const int	BT_SIZEOF_INT = 4
const int	GZIP_ID1 = 31
const int	GZIP_ID2 = 139
const int	CM_DEFLATE = 8
const int	FLG_FEXTRA = 4
const int	OS_UNKNOWN = 255
const int	BGZF_XLEN = 6
const int	BGZF_ID1 = 66
const int	BGZF_ID2 = 67
const int	BGZF_LEN = 2
const int	GZIP_WINDOW_BITS = -15
const int	Z_DEFAULT_MEM_LEVEL = 8
const int	BLOCK_HEADER_LENGTH = 18
const int	BLOCK_FOOTER_LENGTH = 8
const int	MAX_BLOCK_SIZE = 65536
const int	DEFAULT_BLOCK_SIZE = 65536

Typedef Documentation

typedef std::vector<BamAlignment> BamTools::BamAlignmentVector

Definition at line 444 of file BamAux.h.

typedef std::map<uint32_t, ChunkVector> BamTools::BamBinMap

Definition at line 466 of file BamAux.h.

typedef std::vector<ReferenceIndex> BamTools::BamIndex

Definition at line 481 of file BamAux.h.

typedef std::vector<Chunk> BamTools::ChunkVector

Definition at line 465 of file BamAux.h.

typedef std::vector<uint64_t> BamTools::LinearOffsetVector

Definition at line 467 of file BamAux.h.

typedef std::vector<RefData> BamTools::RefVector

Definition at line 443 of file BamAux.h.

Function Documentation

bool BamTools::ChunkLessThan ( const Chunk &  lhs, const Chunk &  rhs  )

inline

Definition at line 461 of file BamAux.h.

Variable Documentation

const int BamTools::BAM_CDEL = 2

Definition at line 33 of file BamAux.h.

const int BamTools::BAM_CHARD_CLIP = 5

Definition at line 36 of file BamAux.h.

const int BamTools::BAM_CIGAR_MASK = ((1 << BAM_CIGAR_SHIFT) - 1)

Definition at line 39 of file BamAux.h.

const int BamTools::BAM_CIGAR_SHIFT = 4

Definition at line 38 of file BamAux.h.

const int BamTools::BAM_CINS = 1

Definition at line 32 of file BamAux.h.

const int BamTools::BAM_CMATCH = 0

Definition at line 31 of file BamAux.h.

const int BamTools::BAM_CORE_SIZE = 32

Definition at line 30 of file BamAux.h.

const int BamTools::BAM_CPAD = 6

Definition at line 37 of file BamAux.h.

const int BamTools::BAM_CREF_SKIP = 3

Definition at line 34 of file BamAux.h.

const int BamTools::BAM_CSOFT_CLIP = 4

Definition at line 35 of file BamAux.h.

const int BamTools::BAM_LIDX_SHIFT = 14

Definition at line 44 of file BamAux.h.

const int BamTools::BAM_MIN_CHUNK_GAP = 32768

Definition at line 43 of file BamAux.h.

const int BamTools::BGZF_ID1 = 66

Definition at line 53 of file BGZF.h.

const int BamTools::BGZF_ID2 = 67

Definition at line 54 of file BGZF.h.

const int BamTools::BGZF_LEN = 2

Definition at line 55 of file BGZF.h.

const int BamTools::BGZF_XLEN = 6

Definition at line 52 of file BGZF.h.

const int BamTools::BLOCK_FOOTER_LENGTH = 8

Definition at line 61 of file BGZF.h.

const int BamTools::BLOCK_HEADER_LENGTH = 18

Definition at line 60 of file BGZF.h.

const int BamTools::BT_SIZEOF_INT = 4

Definition at line 47 of file BamAux.h.

const int BamTools::CM_DEFLATE = 8

Definition at line 49 of file BGZF.h.

const int BamTools::DEFAULT_BLOCK_SIZE = 65536

Definition at line 63 of file BGZF.h.

const int BamTools::FLG_FEXTRA = 4

Definition at line 50 of file BGZF.h.

const int BamTools::GZIP_ID1 = 31

Definition at line 47 of file BGZF.h.

const int BamTools::GZIP_ID2 = 139

Definition at line 48 of file BGZF.h.

const int BamTools::GZIP_WINDOW_BITS = -15

Definition at line 56 of file BGZF.h.

const int BamTools::MAX_BIN = 37450

Definition at line 42 of file BamAux.h.

const int BamTools::MAX_BLOCK_SIZE = 65536

Definition at line 62 of file BGZF.h.

const int BamTools::OS_UNKNOWN = 255

Definition at line 51 of file BGZF.h.

const int BamTools::Z_DEFAULT_MEM_LEVEL = 8

Definition at line 57 of file BGZF.h.