BamTools  2.5.1
Namespaces | Classes | Typedefs | Functions
BamTools Namespace Reference

Contains all BamTools classes & methods. More...

Namespaces

 Algorithms
 Provides convenient classes & methods for working with BAM data.
 
 Constants
 Provides basic constants for handling BAM files.
 

Classes

class  BamAlignment
 The main BAM alignment data structure. More...
 
class  BamIndex
 Provides methods for generating & loading BAM index files. More...
 
class  BamMultiReader
 Convenience class for reading multiple BAM files. More...
 
class  BamReader
 Provides read access to BAM files. More...
 
struct  BamRegion
 Represents a sequential genomic region. More...
 
class  BamWriter
 Provides write access for generating BAM files. More...
 
struct  CigarOp
 Represents a CIGAR alignment operation. More...
 
struct  CustomHeaderTag
 
class  IBamIODevice
 
struct  RaiiBuffer
 
struct  RefData
 Represents a reference sequence entry. More...
 
struct  SamHeader
 Represents the SAM-formatted text header that is part of the BAM file header. More...
 
struct  SamProgram
 Represents a SAM program record. More...
 
class  SamProgramChain
 Sorted container "chain" of SamProgram records. More...
 
struct  SamReadGroup
 Represents a SAM read group entry. More...
 
class  SamReadGroupDictionary
 Container of SamReadGroup entries. More...
 
struct  SamSequence
 Represents a SAM sequence entry. More...
 
class  SamSequenceDictionary
 Container of SamSequence entries. More...
 

Typedefs

typedef std::vector< BamAlignmentBamAlignmentVector
 
typedef std::vector< RefDataRefVector
 convenience typedef for vector of RefData entries More...
 
typedef std::vector< SamProgramSamProgramContainer
 
typedef SamProgramContainer::iterator SamProgramIterator
 
typedef SamProgramContainer::const_iterator SamProgramConstIterator
 
typedef std::vector< SamReadGroupSamReadGroupContainer
 
typedef SamReadGroupContainer::iterator SamReadGroupIterator
 
typedef SamReadGroupContainer::const_iterator SamReadGroupConstIterator
 
typedef std::vector< SamSequenceSamSequenceContainer
 
typedef SamSequenceContainer::iterator SamSequenceIterator
 
typedef SamSequenceContainer::const_iterator SamSequenceConstIterator
 

Functions

template<>
bool BamAlignment::AddTag< std::string > (const std::string &tag, const std::string &type, const std::string &value)
 
template<>
bool BamAlignment::GetTag< std::string > (const std::string &tag, std::string &destination) const
 
API_EXPORT bool FileExists (const std::string &filename)
 returns true if the file exists More...
 
API_EXPORT void SwapEndian_16 (int16_t &x)
 swaps endianness of signed 16-bit integer, in place More...
 
API_EXPORT void SwapEndian_16 (uint16_t &x)
 swaps endianness of unsigned 16-bit integer, in place More...
 
API_EXPORT void SwapEndian_32 (int32_t &x)
 swaps endianness of signed 32-bit integer, in place More...
 
API_EXPORT void SwapEndian_32 (uint32_t &x)
 swaps endianness of unsigned 32-bit integer, in place More...
 
API_EXPORT void SwapEndian_64 (int64_t &x)
 swaps endianness of signed 64-bit integer, in place More...
 
API_EXPORT void SwapEndian_64 (uint64_t &x)
 swaps endianness of unsigned 64-bit integer, in place More...
 
API_EXPORT void SwapEndian_16p (char *data)
 swaps endianness of the next 2 bytes in a buffer, in place More...
 
API_EXPORT void SwapEndian_32p (char *data)
 swaps endianness of the next 4 bytes in a buffer, in place More...
 
API_EXPORT void SwapEndian_64p (char *data)
 swaps endianness of the next 8 bytes in a buffer, in place More...
 
API_EXPORT bool SystemIsBigEndian ()
 checks host architecture's byte order More...
 
API_EXPORT void PackUnsignedInt (char *buffer, unsigned int value)
 stores unsigned integer value in a byte buffer More...
 
API_EXPORT void PackUnsignedShort (char *buffer, unsigned short value)
 stores unsigned short integer value in a byte buffer More...
 
API_EXPORT double UnpackDouble (const char *buffer)
 reads a double value from byte buffer More...
 
API_EXPORT double UnpackDouble (char *buffer)
 reads a double value from byte buffer More...
 
API_EXPORT float UnpackFloat (const char *buffer)
 reads a float value from byte buffer More...
 
API_EXPORT float UnpackFloat (char *buffer)
 reads a float value from byte buffer More...
 
API_EXPORT signed int UnpackSignedInt (const char *buffer)
 reads a signed integer value from byte buffer More...
 
API_EXPORT signed int UnpackSignedInt (char *buffer)
 reads a signed integer value from byte buffer More...
 
API_EXPORT signed short UnpackSignedShort (const char *buffer)
 reads a signed short integer value from byte buffer More...
 
API_EXPORT signed short UnpackSignedShort (char *buffer)
 reads a signed short integer value from byte buffer More...
 
API_EXPORT unsigned int UnpackUnsignedInt (const char *buffer)
 reads an unsigned integer value from byte buffer More...
 
API_EXPORT unsigned int UnpackUnsignedInt (char *buffer)
 reads an unsigned integer value from byte buffer More...
 
API_EXPORT unsigned short UnpackUnsignedShort (const char *buffer)
 reads an unsigned short integer value from byte buffer More...
 
API_EXPORT unsigned short UnpackUnsignedShort (char *buffer)
 reads an unsigned short integer value from byte buffer More...
 
API_EXPORT bool operator== (const SamProgram &lhs, const SamProgram &rhs)
 tests equality by comparing program IDs More...
 
API_EXPORT bool operator== (const SamReadGroup &lhs, const SamReadGroup &rhs)
 tests equality by comparing read group IDs More...
 
API_EXPORT bool operator== (const SamSequence &lhs, const SamSequence &rhs)
 tests equality by comparing sequence names, lengths, & checksums (if available) More...
 

Detailed Description

Contains all BamTools classes & methods.

The BamTools API contained in this namespace contains classes and methods for reading, writing, and manipulating BAM alignment files.

Typedef Documentation

◆ BamAlignmentVector

◆ RefVector

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

convenience typedef for vector of RefData entries

◆ SamProgramConstIterator

typedef SamProgramContainer::const_iterator BamTools::SamProgramConstIterator

◆ SamProgramContainer

◆ SamProgramIterator

typedef SamProgramContainer::iterator BamTools::SamProgramIterator

◆ SamReadGroupConstIterator

typedef SamReadGroupContainer::const_iterator BamTools::SamReadGroupConstIterator

◆ SamReadGroupContainer

◆ SamReadGroupIterator

typedef SamReadGroupContainer::iterator BamTools::SamReadGroupIterator

◆ SamSequenceConstIterator

typedef SamSequenceContainer::const_iterator BamTools::SamSequenceConstIterator

◆ SamSequenceContainer

◆ SamSequenceIterator

typedef SamSequenceContainer::iterator BamTools::SamSequenceIterator

Function Documentation

◆ BamAlignment::AddTag< std::string >()

template<>
bool BamTools::BamAlignment::AddTag< std::string > ( const std::string &  tag,
const std::string &  type,
const std::string &  value 
)
inline

◆ BamAlignment::GetTag< std::string >()

template<>
bool BamTools::BamAlignment::GetTag< std::string > ( const std::string &  tag,
std::string &  destination 
) const
inline

◆ FileExists()

bool BamTools::FileExists ( const std::string &  filename)
inline

returns true if the file exists

◆ operator==() [1/3]

bool BamTools::operator== ( const SamProgram lhs,
const SamProgram rhs 
)
inline

tests equality by comparing program IDs

◆ operator==() [2/3]

bool BamTools::operator== ( const SamReadGroup lhs,
const SamReadGroup rhs 
)
inline

tests equality by comparing read group IDs

◆ operator==() [3/3]

bool BamTools::operator== ( const SamSequence lhs,
const SamSequence rhs 
)
inline

tests equality by comparing sequence names, lengths, & checksums (if available)

◆ PackUnsignedInt()

void BamTools::PackUnsignedInt ( char *  buffer,
unsigned int  value 
)
inline

stores unsigned integer value in a byte buffer

Parameters
[out]bufferdestination buffer
[in]valuevalue to 'pack' in buffer

◆ PackUnsignedShort()

void BamTools::PackUnsignedShort ( char *  buffer,
unsigned short  value 
)
inline

stores unsigned short integer value in a byte buffer

Parameters
[out]bufferdestination buffer
[in]valuevalue to 'pack' in buffer

◆ SwapEndian_16() [1/2]

void BamTools::SwapEndian_16 ( int16_t &  x)
inline

swaps endianness of signed 16-bit integer, in place

◆ SwapEndian_16() [2/2]

void BamTools::SwapEndian_16 ( uint16_t &  x)
inline

swaps endianness of unsigned 16-bit integer, in place

◆ SwapEndian_16p()

void BamTools::SwapEndian_16p ( char *  data)
inline

swaps endianness of the next 2 bytes in a buffer, in place

◆ SwapEndian_32() [1/2]

void BamTools::SwapEndian_32 ( int32_t &  x)
inline

swaps endianness of signed 32-bit integer, in place

◆ SwapEndian_32() [2/2]

void BamTools::SwapEndian_32 ( uint32_t &  x)
inline

swaps endianness of unsigned 32-bit integer, in place

◆ SwapEndian_32p()

void BamTools::SwapEndian_32p ( char *  data)
inline

swaps endianness of the next 4 bytes in a buffer, in place

◆ SwapEndian_64() [1/2]

void BamTools::SwapEndian_64 ( int64_t &  x)
inline

swaps endianness of signed 64-bit integer, in place

◆ SwapEndian_64() [2/2]

void BamTools::SwapEndian_64 ( uint64_t &  x)
inline

swaps endianness of unsigned 64-bit integer, in place

◆ SwapEndian_64p()

void BamTools::SwapEndian_64p ( char *  data)
inline

swaps endianness of the next 8 bytes in a buffer, in place

◆ SystemIsBigEndian()

bool BamTools::SystemIsBigEndian ( )
inline

checks host architecture's byte order

Returns
true if system uses big-endian ordering

◆ UnpackDouble() [1/2]

double BamTools::UnpackDouble ( char *  buffer)
inline

reads a double value from byte buffer

This is an overloaded function.

Parameters
[in]buffersource byte buffer
Returns
the (double) value read from the buffer

◆ UnpackDouble() [2/2]

double BamTools::UnpackDouble ( const char *  buffer)
inline

reads a double value from byte buffer

Parameters
[in]buffersource byte buffer
Returns
the (double) value read from the buffer

◆ UnpackFloat() [1/2]

double BamTools::UnpackFloat ( char *  buffer)
inline

reads a float value from byte buffer

This is an overloaded function.

Parameters
[in]buffersource byte buffer
Returns
the (float) value read from the buffer

◆ UnpackFloat() [2/2]

double BamTools::UnpackFloat ( const char *  buffer)
inline

reads a float value from byte buffer

Parameters
[in]buffersource byte buffer
Returns
the (float) value read from the buffer

◆ UnpackSignedInt() [1/2]

signed int BamTools::UnpackSignedInt ( char *  buffer)
inline

reads a signed integer value from byte buffer

This is an overloaded function.

Parameters
[in]buffersource byte buffer
Returns
the (signed int) value read from the buffer

◆ UnpackSignedInt() [2/2]

signed int BamTools::UnpackSignedInt ( const char *  buffer)
inline

reads a signed integer value from byte buffer

Parameters
[in]buffersource byte buffer
Returns
the (signed int) value read from the buffer

◆ UnpackSignedShort() [1/2]

signed short BamTools::UnpackSignedShort ( char *  buffer)
inline

reads a signed short integer value from byte buffer

This is an overloaded function.

Parameters
[in]buffersource byte buffer
Returns
the (signed short) value read from the buffer

◆ UnpackSignedShort() [2/2]

signed short BamTools::UnpackSignedShort ( const char *  buffer)
inline

reads a signed short integer value from byte buffer

Parameters
[in]buffersource byte buffer
Returns
the (signed short) value read from the buffer

◆ UnpackUnsignedInt() [1/2]

unsigned int BamTools::UnpackUnsignedInt ( char *  buffer)
inline

reads an unsigned integer value from byte buffer

This is an overloaded function.

Parameters
[in]buffersource byte buffer
Returns
the (unsigned int) value read from the buffer

◆ UnpackUnsignedInt() [2/2]

unsigned int BamTools::UnpackUnsignedInt ( const char *  buffer)
inline

reads an unsigned integer value from byte buffer

Parameters
[in]buffersource byte buffer
Returns
the (unsigned int) value read from the buffer

◆ UnpackUnsignedShort() [1/2]

unsigned short BamTools::UnpackUnsignedShort ( char *  buffer)
inline

reads an unsigned short integer value from byte buffer

This is an overloaded function.

Parameters
[in]buffersource byte buffer
Returns
the (unsigned short) value read from the buffer

◆ UnpackUnsignedShort() [2/2]

unsigned short BamTools::UnpackUnsignedShort ( const char *  buffer)
inline

reads an unsigned short integer value from byte buffer

Parameters
[in]buffersource byte buffer
Returns
the (unsigned short) value read from the buffer