BamTools
2.5.1
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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< BamAlignment > | BamAlignmentVector |
typedef std::vector< RefData > | RefVector |
convenience typedef for vector of RefData entries More... | |
typedef std::vector< SamProgram > | SamProgramContainer |
typedef SamProgramContainer::iterator | SamProgramIterator |
typedef SamProgramContainer::const_iterator | SamProgramConstIterator |
typedef std::vector< SamReadGroup > | SamReadGroupContainer |
typedef SamReadGroupContainer::iterator | SamReadGroupIterator |
typedef SamReadGroupContainer::const_iterator | SamReadGroupConstIterator |
typedef std::vector< SamSequence > | SamSequenceContainer |
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... | |
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 std::vector<BamAlignment> BamTools::BamAlignmentVector |
typedef std::vector<RefData> BamTools::RefVector |
convenience typedef for vector of RefData entries
typedef SamProgramContainer::const_iterator BamTools::SamProgramConstIterator |
typedef std::vector<SamProgram> BamTools::SamProgramContainer |
typedef SamProgramContainer::iterator BamTools::SamProgramIterator |
typedef SamReadGroupContainer::const_iterator BamTools::SamReadGroupConstIterator |
typedef std::vector<SamReadGroup> BamTools::SamReadGroupContainer |
typedef SamReadGroupContainer::iterator BamTools::SamReadGroupIterator |
typedef SamSequenceContainer::const_iterator BamTools::SamSequenceConstIterator |
typedef std::vector<SamSequence> BamTools::SamSequenceContainer |
typedef SamSequenceContainer::iterator BamTools::SamSequenceIterator |
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returns true if the file exists
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tests equality by comparing program IDs
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tests equality by comparing read group IDs
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tests equality by comparing sequence names, lengths, & checksums (if available)
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stores unsigned integer value in a byte buffer
[out] | buffer | destination buffer |
[in] | value | value to 'pack' in buffer |
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stores unsigned short integer value in a byte buffer
[out] | buffer | destination buffer |
[in] | value | value to 'pack' in buffer |
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swaps endianness of signed 16-bit integer, in place
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inline |
swaps endianness of unsigned 16-bit integer, in place
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inline |
swaps endianness of the next 2 bytes in a buffer, in place
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inline |
swaps endianness of signed 32-bit integer, in place
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inline |
swaps endianness of unsigned 32-bit integer, in place
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inline |
swaps endianness of the next 4 bytes in a buffer, in place
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inline |
swaps endianness of signed 64-bit integer, in place
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inline |
swaps endianness of unsigned 64-bit integer, in place
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inline |
swaps endianness of the next 8 bytes in a buffer, in place
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inline |
checks host architecture's byte order
true
if system uses big-endian ordering
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inline |
reads a double value from byte buffer
This is an overloaded function.
[in] | buffer | source byte buffer |
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inline |
reads a double value from byte buffer
[in] | buffer | source byte buffer |
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inline |
reads a float value from byte buffer
This is an overloaded function.
[in] | buffer | source byte buffer |
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inline |
reads a float value from byte buffer
[in] | buffer | source byte buffer |
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inline |
reads a signed integer value from byte buffer
This is an overloaded function.
[in] | buffer | source byte buffer |
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inline |
reads a signed integer value from byte buffer
[in] | buffer | source byte buffer |
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inline |
reads a signed short integer value from byte buffer
This is an overloaded function.
[in] | buffer | source byte buffer |
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inline |
reads a signed short integer value from byte buffer
[in] | buffer | source byte buffer |
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inline |
reads an unsigned integer value from byte buffer
This is an overloaded function.
[in] | buffer | source byte buffer |
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inline |
reads an unsigned integer value from byte buffer
[in] | buffer | source byte buffer |
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inline |
reads an unsigned short integer value from byte buffer
This is an overloaded function.
[in] | buffer | source byte buffer |
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inline |
reads an unsigned short integer value from byte buffer
[in] | buffer | source byte buffer |