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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< RefDataRefVector
 
typedef std::vector< BamAlignmentBamAlignmentVector
 
typedef std::vector< ChunkChunkVector
 
typedef std::map< uint32_t,
ChunkVector
BamBinMap
 
typedef std::vector< uint64_tLinearOffsetVector
 
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

Definition at line 444 of file BamAux.h.

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.