Classes
class	AMOS::IBankable_t
	Interface for classes that can be stored in an AMOS bank. More...
class	AMOS::Bank_t
	An AMOS data bank for efficiently storing Bankable data types. More...
class	AMOS::Bank_t::BankPartition_t
	A single partition of the file-based bank. More...
class	AMOS::BankStream_t
	Provides stream functionality for an AMOS data bank. More...
class	AMOS::Contig_t
	A tiling of assembled sequence reads. More...
class	AMOS::ContigEdge_t
	Reliable linking information between two contigs. More...
class	AMOS::ContigLink_t
	Linking information between two contigs. More...
struct	AMOS::Distribution_t
	A set of statistics that define a distribution. More...
struct	AMOS::Range_t
	A gapped coordinate range. More...
struct	AMOS::Tile_t
	A singe sequence's location and orientation in a larger sequence. More...
class	AMOS::IEdge_t
	Interface for Edge_t. More...
class	AMOS::Edge_t
	Reliable linking information between two nodes. More...
class	AMOS::Exception_t
	The base AMOS excpetion class. More...
class	AMOS::AlignmentException_t
	An exception for alignment failures. More...
class	AMOS::AllocException_t
	An exception for alloc failures, better than std::bad_alloc. More...
class	AMOS::ArgumentException_t
	An exception for invalid arguments. More...
class	AMOS::IOException_t
	An exception for IO errors. More...
class	AMOS::Feature_t
	Notes remarkable features of other objects. More...
class	AMOS::Fragment_t
	Single piece of DNA. More...
class	AMOS::Group_t
	A homogenous grouping of AMOS objects. More...
class	AMOS::IDMap_t
	An IID/EID double hash for mapping IIDs and EIDs to BIDs. More...
struct	AMOS::IDMap_t::HashTriple_t
	HashTriple for IDMap. More...
struct	AMOS::IDMap_t::HashNode_t
	HashNode for IDMap.
class	AMOS::IDMap_t::iterator
	iterator for moving through the map
class	AMOS::IDMap_t::const_iterator
	const_iterator for moving through the map More...
class	AMOS::Index_t
	An association index between two types of AMOS objects. More...
struct	AMOS::BankFlags_t
	8 bit flag set for IBankable types More...
class	AMOS::Kmer_t
	String of K bases present in the assembly. More...
class	AMOS::Layout_t
	A layout of sequences. More...
class	AMOS::Library_t
	A collection of cloned, size-controlled DNA molecules. More...
class	AMOS::Link_t
	Linking information between two nodes, such as between contigs. More...
class	AMOS::Message_t
	A generic AMOS message object for reading and writing data. More...
class	AMOS::IMessagable_t
	Interface for classes that can interpret messages. More...
class	AMOS::Overlap_t
	An overlap relation between to sequencing reads. More...
class	AMOS::Read_t
	A DNA sequencing read. More...
class	AMOS::Scaffold_t
	A ordered, oriented and positioned list of contigs. More...
class	AMOS::ScaffoldEdge_t
	Reliable linking information between two scaffolds. More...
class	AMOS::ScaffoldLink_t
	Linking information between two scaffolds. More...
class	AMOS::Sequence_t
	Sequence bases with quality scores. More...
class	AMOS::Universal_t
	A universal base class that can be used by Banks or Messages. More...
class	AMOS::UniversalSet_t
	A non-redundant, complete collection of Universal objects. More...
class	AMOS::UniversalSet_t::iterator
class	AMOS::UniversalSet_t::const_iterator
class	AMOS::BankSet_t
	A non-redundant, complete collection of AMOS banks. More...
class	AMOS::BankSet_t::iterator
class	AMOS::BankSet_t::const_iterator
class	AMOS::BankStreamSet_t
	A non-redundant, complete collection of AMOS banks. More...
class	AMOS::BankStreamSet_t::iterator
class	AMOS::BankStreamSet_t::const_iterator
Typedefs
typedef uint8_t	BankMode_t
typedef Range_t	Ordered_Range_t
typedef char	FeatureType_t
typedef char	FragmentType_t
typedef uint32_t	ID_t
	ID type for iid's.
typedef uint32_t	NCode_t
	unique integer code for dynamic typing
typedef uint32_t	SD_t
	standard deviation type
typedef int32_t	Size_t
	size type (for links,etc)
typedef Size_t	Pos_t
	position type (in a sequence,etc)
typedef char	Status_t
	status type
typedef char	LinkType_t
typedef char	LinkAdjacency_t
typedef char	OverlapAdjacency_t
typedef char	ReadType_t
Functions
bool	BankExists (NCode_t ncode, const std::string &dir)
	Checks for the accessibility of a bank with certain type.
void	PrintBankVersion (const char *s)
	Prints the bank version a program is compatible with.
Range_t	operator & (Range_t a, Range_t b)
	An intersection operator for Ranges.
Range_t	operator| (Range_t a, Range_t b)
	A union operator for Ranges.
bool	operator== (const Range_t &a, const Range_t &b)
	An equality operator for Ranges.
bool	operator!= (const Range_t &a, const Range_t &b)
bool	operator== (const Distribution_t &a, const Distribution_t &b)
	An equality operator for Distributions.
bool	operator!= (const Distribution_t &a, const Distribution_t &b)
bool	operator== (const Tile_t &a, const Tile_t &b)
	An equality operator for Tiles.
bool	operator!= (const Tile_t &a, const Tile_t &b)
void	WrapString (std::ostream &out, const std::string &s, int per)
	Inserts a newline every 'per' characters when writing to stream.
std::ostream &	operator<< (std::ostream &out, const Exception_t &e)
	Dump Exception_t info to an ostream.
std::ostream &	operator<< (std::ostream &out, const std::exception &e)
	Dump exception info to an ostream.
char	Qual2Char (uint8_t qual)
	Converts a quality int into a printable character.
uint8_t	Char2Qual (char qual)
	Converts a printable quality character to an int.
std::string	Decode (NCode_t ncode)
	Converts an NCode integer to an AMOS message/field type.
NCode_t	Encode (const std::string &str)
	Converts an AMOS message/field type to an NCode integer.
std::ostream &	operator<< (std::ostream &o, Read_t &read)
	Dump read object to ostream.
void *	SafeCalloc (size_t num, size_t size)
	Safe calloc wrapper.
void *	SafeMalloc (size_t size)
	Safe malloc wrapper.
void *	SafeRealloc (void *P, size_t size)
	Safe realloc wrapper.
char *	SafeStrdup (const char *str)
	Safe strdup wrapper.
char	Complement (char ch)
	Returns the DNA complement of an IUPAC character.
void	ReverseComplement (std::string &str)
	Takes the DNA reverse complement of an IUPAC string.
void	ReverseComplement (char *str)
	Takes the DNA reverse complement of an IUPAC string.
void	Reverse (std::string &str)
	Reverses the contents of a string.
void	Reverse (char *str)
	Reverses the contents of a string.
void	writeLE (std::ostream &out, const uint8_t *i)
	Writes an 8-bit int in little-endian byte order.
void	writeLE (std::ostream &out, const int8_t *i)
void	writeLE (std::ostream &out, const BankFlags_t *i)
void	writeLE (std::ostream &out, const uint16_t *i)
	Writes a 16-bit int in little-endian byte order.
void	writeLE (std::ostream &out, const int16_t *i)
void	writeLE (std::ostream &out, const uint32_t *i)
	Writes a 32-bit int in little-endian byte order.
void	writeLE (std::ostream &out, const int32_t *i)
void	writeLE (std::ostream &out, const uint64_t *i)
	Writes a 64-bit int in little-endian byte order.
void	writeLE (std::ostream &out, const int64_t *i)
void	readLE (std::istream &in, uint8_t *i)
	Reads a little-endian 8-bit int.
void	readLE (std::istream &in, int8_t *i)
void	readLE (std::istream &in, BankFlags_t *i)
void	readLE (std::istream &in, uint16_t *i)
	Reads a little-endian 16-bit int.
void	readLE (std::istream &in, int16_t *i)
void	readLE (std::istream &in, uint32_t *i)
	Reads a little-endian 32-bit int.
void	readLE (std::istream &in, int32_t *i)
void	readLE (std::istream &in, uint64_t *i)
	Reads a little-endian 64-bit int.
void	readLE (std::istream &in, int64_t *i)
Variables
const BankMode_t	B_READ = 0x1
	protected reading mode
const BankMode_t	B_WRITE = 0x2
	protected writing mode
const BankMode_t	B_SPY = 0x4
	unprotected reading mode, overrides all other modes
const uint8_t	NCODE_SIZE = 3
	length of the NCode strings
const NCode_t	NULL_NCODE = 0
	NULL NCode definition.
const ID_t	NULL_ID = 0
	NULL ID definition.
const Status_t	NULL_STATUS = 0
	NULL status definition.
const char	MIN_QUALITY = '0'
	min quality score definition
const char	MAX_QUALITY = '0' + 63
	max quality score definition
const char	NULL_CHAR = '\0'
	null char
const char	NL_CHAR = '\n'
	newline char
const std::string	NULL_STRING = &NULL_CHAR
	null string
const ID_t	MAX_ID = ~((uint32_t)0)
	(unsigned 32bit int)
const Size_t	MAX_SIZE = ~((uint32_t)0) >> 1
	( signed 32bit int)
const Pos_t	MAX_POS = ~((uint32_t)0) >> 1
	( signed 32bit int)
const char	E_ADD = 'A'
const char	E_DELETE = 'D'
const char	E_REPLACE = 'R'
const NCode_t	F_NULL = Encode ("nul")
const NCode_t	F_AHANG = Encode ("ahg")
const NCode_t	F_ACTION = Encode ("act")
const NCode_t	F_ADJACENCY = Encode ("adj")
const NCode_t	F_BASEPOSITION = Encode ("bcp")
const NCode_t	F_BHANG = Encode ("bhg")
const NCode_t	F_BID = Encode ("bid")
const NCode_t	F_CLEAR = Encode ("clr")
const NCode_t	F_COMMENT = Encode ("com")
const NCode_t	F_COUNT = Encode ("cnt")
const NCode_t	F_EID = Encode ("eid")
const NCode_t	F_EDGE = Encode ("edg")
const NCode_t	F_FLAG = Encode ("flg")
const NCode_t	F_FRAGMENT = Encode ("frg")
const NCode_t	F_GAPS = Encode ("gap")
const NCode_t	F_IID = Encode ("iid")
const NCode_t	F_LIBRARY = Encode ("lib")
const NCode_t	F_LINK = Encode ("lnk")
const NCode_t	F_MAP = Encode ("map")
const NCode_t	F_MEAN = Encode ("mea")
const NCode_t	F_MEMBER = Encode ("mbr")
const NCode_t	F_NODES = Encode ("nds")
const NCode_t	F_OBJECT = Encode ("obj")
const NCode_t	F_OFFSET = Encode ("off")
const NCode_t	F_POSITION = Encode ("pos")
const NCode_t	F_QUALITY = Encode ("qlt")
const NCode_t	F_QUALITYCLEAR = Encode ("qcr")
const NCode_t	F_READS = Encode ("rds")
const NCode_t	F_SCORE = Encode ("scr")
const NCode_t	F_SEQUENCE = Encode ("seq")
const NCode_t	F_SD = Encode ("std")
const NCode_t	F_SIZE = Encode ("sze")
const NCode_t	F_SOURCE = Encode ("src")
const NCode_t	F_STATUS = Encode ("sts")
const NCode_t	F_TYPE = Encode ("typ")
const NCode_t	F_VECTORCLEAR = Encode ("vcr")
const NCode_t	M_NULL = Encode ("NUL")
const NCode_t	M_UNIVERSAL = Encode ("UNV")
const NCode_t	M_CONTIG = Encode ("CTG")
const NCode_t	M_CONTIGEDGE = Encode ("CTE")
const NCode_t	M_CONTIGLINK = Encode ("CTL")
const NCode_t	M_DISTRIBUTION = Encode ("DST")
const NCode_t	M_EDGE = Encode ("EDG")
const NCode_t	M_FEATURE = Encode ("FEA")
const NCode_t	M_FRAGMENT = Encode ("FRG")
const NCode_t	M_GROUP = Encode ("GRP")
const NCode_t	M_KMER = Encode ("KMR")
const NCode_t	M_LAYOUT = Encode ("LAY")
const NCode_t	M_LIBRARY = Encode ("LIB")
const NCode_t	M_LINK = Encode ("LNK")
const NCode_t	M_IDMAP = Encode ("MAP")
const NCode_t	M_INDEX = Encode ("IDX")
const NCode_t	M_OVERLAP = Encode ("OVL")
const NCode_t	M_READ = Encode ("RED")
const NCode_t	M_SCAFFOLD = Encode ("SCF")
const NCode_t	M_SCAFFOLDEDGE = Encode ("SCE")
const NCode_t	M_SCAFFOLDLINK = Encode ("SCL")
const NCode_t	M_SEQUENCE = Encode ("SEQ")
const NCode_t	M_TILE = Encode ("TLE")

---

Typedef Documentation

typedef uint8_t AMOS::BankMode_t

Definition at line 34 of file Bank_AMOS.hh. Referenced by AMOS::BankStream_t::create(), AMOS::Bank_t::create(), AMOS::BankStream_t::open(), AMOS::Bank_t::open(), and AMOS::Bank_t::setMode().

typedef char AMOS::FeatureType_t

Definition at line 20 of file Feature_AMOS.hh. Referenced by AMOS::Feature_t::getType(), and AMOS::Feature_t::setType().

typedef char AMOS::FragmentType_t

Definition at line 20 of file Fragment_AMOS.hh. Referenced by AMOS::Fragment_t::getType(), and AMOS::Fragment_t::setType().

typedef uint32_t AMOS::ID_t

ID type for iid's. Definition at line 24 of file inttypes_AMOS.hh. Referenced by AMOS::Bank_t::assignEID(), AMOS::Bank_t::assignIID(), AMOS::Bank_t::concat(), AMOS::Index_t::count(), AMOS::IDMap_t::exists(), AMOS::BankStream_t::existsIID(), AMOS::Bank_t::existsIID(), AMOS::Bank_t::fetch(), AMOS::Bank_t::fetchBID(), AMOS::Read_t::getFragment(), AMOS::IBankable_t::getIID(), AMOS::Fragment_t::getLibrary(), AMOS::BankStream_t::getMaxIID(), AMOS::Bank_t::getMaxIID(), AMOS::Link_t::getNodes(), AMOS::Bank_t::getPartition(), AMOS::IDMap_t::HashTriple_t::HashTriple_t(), AMOS::BankStream_t::ignore(), AMOS::Index_t::insert(), AMOS::IDMap_t::insert(), AMOS::Index_t::isMulti(), AMOS::Bank_t::localizeBID(), AMOS::Index_t::lookup(), AMOS::Index_t::lookupAll(), AMOS::IDMap_t::lookupBID(), AMOS::BankStream_t::lookupBID(), AMOS::Bank_t::lookupBID(), AMOS::IDMap_t::lookupEID(), AMOS::BankStream_t::lookupEID(), AMOS::Bank_t::lookupEID(), AMOS::IDMap_t::lookupIID(), AMOS::BankStream_t::lookupIID(), AMOS::Bank_t::lookupIID(), main(), AMOS::Bank_t::openPartition(), AMOS::BankStream_t::operator>>(), AMOS::IDMap_t::read(), AMOS::Scaffold_t::readMessage(), AMOS::Kmer_t::readMessage(), AMOS::IDMap_t::readMessage(), AMOS::Group_t::readMessage(), AMOS::IEdge_t::readMessage(), AMOS::Index_t::remove(), AMOS::IDMap_t::remove(), AMOS::Bank_t::remove(), AMOS::Bank_t::removeBID(), AMOS::Bank_t::replace(), AMOS::Bank_t::replaceBID(), AMOS::BankStream_t::seekg(), AMOS::Read_t::setFragment(), AMOS::IBankable_t::setIID(), AMOS::Fragment_t::setLibrary(), AMOS::IEdge_t::setLinks(), AMOS::Bank_t::syncIFO(), AMOS::BankStream_t::tellg(), and AMOS::BankStream_t::tellp().

typedef char AMOS::LinkAdjacency_t

Definition at line 22 of file Link_AMOS.hh. Referenced by AMOS::Link_t::flip(), AMOS::Link_t::getAdjacency(), and AMOS::Link_t::setAdjacency().

typedef char AMOS::LinkType_t

Definition at line 21 of file Link_AMOS.hh. Referenced by AMOS::Link_t::getType(), and AMOS::Link_t::setType().

typedef uint32_t AMOS::NCode_t

unique integer code for dynamic typing Definition at line 25 of file inttypes_AMOS.hh. Referenced by AMOS::Bank_t::Bank_t(), BankExists(), AMOS::BankStream_t::BankStream_t(), Decode(), Encode(), AMOS::BankStreamSet_t::exists(), AMOS::BankSet_t::exists(), AMOS::UniversalSet_t::exists(), AMOS::Message_t::exists(), AMOS::Message_t::getField(), AMOS::Group_t::getMemberType(), AMOS::Message_t::getMessageCode(), AMOS::Universal_t::getNCode(), AMOS::Sequence_t::getNCode(), AMOS::ScaffoldLink_t::getNCode(), AMOS::ScaffoldEdge_t::getNCode(), AMOS::Scaffold_t::getNCode(), AMOS::Read_t::getNCode(), AMOS::Overlap_t::getNCode(), AMOS::Link_t::getNCode(), AMOS::Library_t::getNCode(), AMOS::Layout_t::getNCode(), AMOS::Kmer_t::getNCode(), AMOS::Index_t::getNCode(), AMOS::IDMap_t::getNCode(), AMOS::Group_t::getNCode(), AMOS::Fragment_t::getNCode(), AMOS::Feature_t::getNCode(), AMOS::Edge_t::getNCode(), AMOS::Tile_t::getNCode(), AMOS::Distribution_t::getNCode(), AMOS::ContigLink_t::getNCode(), AMOS::ContigEdge_t::getNCode(), AMOS::Contig_t::getNCode(), AMOS::ScaffoldLink_t::getNodeType(), AMOS::Link_t::getNodeType(), AMOS::ContigLink_t::getNodeType(), AMOS::IDMap_t::getType(), AMOS::BankStream_t::getType(), AMOS::Bank_t::getType(), AMOS::Index_t::Index_t(), AMOS::BankStreamSet_t::operator[](), AMOS::BankSet_t::operator[](), AMOS::UniversalSet_t::operator[](), AMOS::Message_t::operator[](), AMOS::Message_t::removeField(), AMOS::IDMap_t::resize(), AMOS::Message_t::setField(), AMOS::Group_t::setMemberType(), AMOS::Message_t::setMessageCode(), AMOS::Link_t::setNodeType(), AMOS::Index_t::setType(), AMOS::IDMap_t::setType(), AMOS::Message_t::skip(), and AMOS::Bank_t::syncIFO().

typedef Range_t AMOS::Ordered_Range_t

Definition at line 453 of file datatypes_AMOS.hh.

typedef char AMOS::OverlapAdjacency_t

Definition at line 20 of file Overlap_AMOS.hh. Referenced by AMOS::Overlap_t::flip(), AMOS::Overlap_t::getAdjacency(), and AMOS::Overlap_t::setAdjacency().

typedef Size_t AMOS::Pos_t

position type (in a sequence,etc) Definition at line 28 of file inttypes_AMOS.hh. Referenced by AMOS::Sequence_t::compress(), AMOS::Contig_t::gap2ungap(), AMOS::Sequence_t::getBase(), AMOS::Kmer_t::getBase(), AMOS::Range_t::getBegin(), AMOS::Range_t::getEnd(), AMOS::Read_t::getFragmentPosition(), AMOS::Range_t::getHi(), AMOS::Range_t::getLo(), AMOS::Sequence_t::getQualString(), AMOS::Sequence_t::getSeqString(), AMOS::Kmer_t::getSeqString(), AMOS::Scaffold_t::getSpan(), AMOS::Layout_t::getSpan(), AMOS::Contig_t::getSpan(), AMOS::Contig_t::getUngappedLength(), AMOS::Contig_t::getUngappedQualString(), AMOS::Contig_t::getUngappedSeqString(), operator &(), operator|(), AMOS::Range_t::Range_t(), AMOS::Tile_t::readMessage(), AMOS::Scaffold_t::readRecord(), AMOS::Read_t::readRecord(), AMOS::Layout_t::readRecord(), AMOS::Kmer_t::readRecord(), AMOS::Index_t::readRecord(), AMOS::Group_t::readRecord(), AMOS::IEdge_t::readRecord(), AMOS::Tile_t::readRecord(), AMOS::Contig_t::readRecord(), AMOS::Sequence_t::setBase(), AMOS::Kmer_t::setBase(), AMOS::Range_t::setBegin(), AMOS::Range_t::setEnd(), AMOS::Read_t::setFragmentPosition(), AMOS::Range_t::setRange(), AMOS::Kmer_t::setSeqString(), AMOS::Sequence_t::setSequence(), AMOS::Range_t::swap(), AMOS::Sequence_t::uncompress(), AMOS::Contig_t::ungap2gap(), AMOS::Sequence_t::writeMessage(), AMOS::Scaffold_t::writeMessage(), AMOS::Layout_t::writeMessage(), AMOS::Contig_t::writeMessage(), AMOS::Scaffold_t::writeRecord(), AMOS::Read_t::writeRecord(), AMOS::Layout_t::writeRecord(), AMOS::Kmer_t::writeRecord(), AMOS::Group_t::writeRecord(), AMOS::IEdge_t::writeRecord(), AMOS::Tile_t::writeRecord(), and AMOS::Contig_t::writeRecord().

typedef char AMOS::ReadType_t

Definition at line 21 of file Read_AMOS.hh. Referenced by AMOS::Read_t::getType(), and AMOS::Read_t::setType().

typedef uint32_t AMOS::SD_t

standard deviation type Definition at line 26 of file inttypes_AMOS.hh. Referenced by AMOS::Link_t::getSD(), and AMOS::Link_t::setSD().

typedef int32_t AMOS::Size_t

size type (for links,etc) Definition at line 27 of file inttypes_AMOS.hh. Referenced by AMOS::Bank_t::appendBID(), AMOS::Bank_t::BankPartition_t::BankPartition_t(), AMOS::Bank_t::clean(), AMOS::Bank_t::clear(), AMOS::Bank_t::close(), AMOS::Bank_t::concat(), AMOS::Index_t::count(), AMOS::Message_t::countFields(), AMOS::Message_t::countSubMessages(), AMOS::Overlap_t::flip(), AMOS::Overlap_t::getAhang(), AMOS::Overlap_t::getBhang(), AMOS::IDMap_t::getBuckets(), AMOS::Tile_t::getGappedLength(), AMOS::BankStream_t::getIDMapSize(), AMOS::Bank_t::getIDMapSize(), AMOS::Bank_t::getIndexSize(), AMOS::Sequence_t::getLength(), AMOS::Range_t::getLength(), AMOS::BankStreamSet_t::getSize(), AMOS::BankSet_t::getSize(), AMOS::UniversalSet_t::getSize(), AMOS::Link_t::getSize(), AMOS::Index_t::getSize(), AMOS::IDMap_t::getSize(), AMOS::Fragment_t::getSize(), AMOS::BankStream_t::getSize(), AMOS::Bank_t::getSize(), AMOS::Scaffold_t::getSpan(), AMOS::Layout_t::getSpan(), AMOS::Contig_t::getSpan(), AMOS::Contig_t::getUngappedLength(), AMOS::IDMap_t::IDMap_t(), AMOS::BankStream_t::ignore(), AMOS::Bank_t::openPartition(), AMOS::BankStream_t::operator<<(), AMOS::Kmer_t::operator=(), AMOS::BankStream_t::operator>>(), AMOS::IDMap_t::read(), AMOS::Index_t::readMessage(), AMOS::IDMap_t::readMessage(), AMOS::Scaffold_t::readRecord(), AMOS::Read_t::readRecord(), AMOS::Layout_t::readRecord(), AMOS::Kmer_t::readRecord(), AMOS::Index_t::readRecord(), AMOS::Group_t::readRecord(), AMOS::IEdge_t::readRecord(), AMOS::Tile_t::readRecord(), AMOS::Contig_t::readRecord(), AMOS::Index_t::remove(), AMOS::Bank_t::replaceBID(), AMOS::IDMap_t::resize(), AMOS::Overlap_t::setAhang(), AMOS::Overlap_t::setBhang(), AMOS::Kmer_t::setSeqString(), AMOS::Sequence_t::setSequence(), AMOS::Link_t::setSize(), AMOS::Fragment_t::setSize(), AMOS::Bank_t::syncIFO(), AMOS::Contig_t::ungap2gap(), AMOS::Sequence_t::writeMessage(), AMOS::Index_t::writeMessage(), AMOS::Scaffold_t::writeRecord(), AMOS::Read_t::writeRecord(), AMOS::Layout_t::writeRecord(), AMOS::Kmer_t::writeRecord(), AMOS::Index_t::writeRecord(), AMOS::Group_t::writeRecord(), AMOS::IEdge_t::writeRecord(), AMOS::Tile_t::writeRecord(), and AMOS::Contig_t::writeRecord().

typedef char AMOS::Status_t

status type Definition at line 29 of file inttypes_AMOS.hh. Referenced by AMOS::Universal_t::getStatus(), and AMOS::Universal_t::setStatus().

---

Function Documentation

bool AMOS::BankExists (  NCode_t  ncode, const std::string &  dir )

Checks for the accessibility of a bank with certain type. Only checks for the existence and readability of the info store, does not perform any validity checking on the other partitions. Parameters: ncode  The type of bank to look for dir  The directory in which to look Returns: true if IFO store exists with read permissions, else false Definition at line 1030 of file Bank_AMOS.cc. References Decode(), and NCode_t.

uint8_t Char2Qual (  char  qual  )  [inline]

Converts a printable quality character to an int. Parameters: qual  Character quality representation Returns: Integer quality representation Definition at line 64 of file inttypes_AMOS.hh. References MIN_QUALITY. Referenced by AMOS::Sequence_t::compress().

char AMOS::Complement (  char  ch  )

Returns the DNA complement of an IUPAC character. Complement-able IUPAC characters are ACGTUMRWSYKVHDB, while NX*- are also acceptable but are self-complementary. Characters other than these will throw an exception. Parameters: ch  The character to take the complement of Exceptions: ArgumentException_t  if ch is an invalid character Returns: void Definition at line 20 of file utility_AMOS.cc. References AMOS_THROW_ARGUMENT. Referenced by ReverseComplement().

std::string Decode (  NCode_t  ncode  )  [inline]

Converts an NCode integer to an AMOS message/field type. Parameters: ncode  The NCode to translate to a string Returns: String representation of the NCode Definition at line 76 of file inttypes_AMOS.hh. References NCode_t. Referenced by BankExists(), AMOS::Bank_t::create(), AMOS::Bank_t::exists(), AMOS::Message_t::getField(), main(), AMOS::Bank_t::open(), AMOS::BankStreamSet_t::operator[](), AMOS::BankSet_t::operator[](), AMOS::UniversalSet_t::operator[](), AMOS::Message_t::read(), AMOS::Bank_t::syncIFO(), AMOS::Message_t::write(), AMOS::IDMap_t::write(), AMOS::Link_t::writeMessage(), AMOS::Index_t::writeMessage(), AMOS::IDMap_t::writeMessage(), AMOS::Group_t::writeMessage(), AMOS::Fragment_t::writeMessage(), and AMOS::Feature_t::writeMessage().

NCode_t Encode (  const std::string &  str  )  [inline]

Converts an AMOS message/field type to an NCode integer. Parameters: str  The NCode string equivalent Precondition: str is of proper NCode length, i.e. str . size( ) == NCODE_SIZE Returns: NCode of the string Definition at line 91 of file inttypes_AMOS.hh. References NCode_t. Referenced by AMOS::Bank_t::Bank_t(), AMOS::Message_t::exists(), AMOS::Message_t::getField(), AMOS::BankStreamSet_t::operator[](), AMOS::BankSet_t::operator[](), AMOS::UniversalSet_t::operator[](), AMOS::IDMap_t::read(), AMOS::Link_t::readMessage(), AMOS::Index_t::readMessage(), AMOS::IDMap_t::readMessage(), AMOS::Group_t::readMessage(), AMOS::Fragment_t::readMessage(), AMOS::Feature_t::readMessage(), AMOS::Message_t::removeField(), AMOS::Message_t::setField(), AMOS::Message_t::setMessageCode(), and AMOS::Message_t::skip().

Range_t AMOS::operator & (  Range_t  a, Range_t  b )

An intersection operator for Ranges. Returns the (foward) intersection of two overlapping ranges. Parameters: a  Range A b  Range B Returns: The intersection of Range A and B or [0,0) if no overlap Definition at line 253 of file datatypes_AMOS.cc. References Pos_t.

bool AMOS::operator!= (  const Tile_t &  a, const Tile_t &  b )

Definition at line 334 of file datatypes_AMOS.cc.

bool AMOS::operator!= (  const Distribution_t &  a, const Distribution_t &  b )

Definition at line 320 of file datatypes_AMOS.cc.

bool AMOS::operator!= (  const Range_t &  a, const Range_t &  b )

Definition at line 308 of file datatypes_AMOS.cc.

ostream & AMOS::operator<< (  std::ostream &  o, Read_t &  read )

Dump read object to ostream. Definition at line 269 of file Read_AMOS.cc. References AMOS::Range_t::begin, AMOS::Range_t::end, AMOS::Read_t::getClearRange(), AMOS::Universal_t::getComment(), AMOS::IBankable_t::getIID(), AMOS::Sequence_t::getQualString(), AMOS::Sequence_t::getSeqString(), and WrapString().

std::ostream& operator<< (  std::ostream &  out, const std::exception &  e )  [inline]

Dump exception info to an ostream. Definition at line 263 of file exceptions_AMOS.hh.

std::ostream& operator<< (  std::ostream &  out, const Exception_t &  e )  [inline]

Dump Exception_t info to an ostream. Definition at line 251 of file exceptions_AMOS.hh.

bool AMOS::operator== (  const Tile_t &  a, const Tile_t &  b )

An equality operator for Tiles. Returns true if distributions have identical values Parameters: a  Tile A b  Tile B Returns: true if distributions have identical values Definition at line 327 of file datatypes_AMOS.cc.

bool AMOS::operator== (  const Distribution_t &  a, const Distribution_t &  b )

An equality operator for Distributions. Returns true if distributions have identical values Parameters: a  Distribution A b  Distribution B Returns: true if distributions have identical values Definition at line 315 of file datatypes_AMOS.cc.

bool AMOS::operator== (  const Range_t &  a, const Range_t &  b )

An equality operator for Ranges. Returns true if the two ranges have equal begin and end values. Parameters: a  Range A b  Range B Returns: true if a.begin == b.begin && a.end == b.end, else false Definition at line 304 of file datatypes_AMOS.cc.

Range_t AMOS::operator| (  Range_t  a, Range_t  b )

A union operator for Ranges. Returns the union of two overlapping ranges Parameters: a  Range A b  Range B Returns: The union of Range A and B or [0,0) if no overlap Definition at line 279 of file datatypes_AMOS.cc. References Pos_t.

void AMOS::PrintBankVersion (  const char *  s  )

Prints the bank version a program is compatible with. Parameters: s  The program name Returns: void Definition at line 1041 of file Bank_AMOS.cc.

char Qual2Char (  uint8_t  qual  )  [inline]

Converts a quality int into a printable character. Parameters: qual  Integer quality representation Returns: Printable quality character Definition at line 52 of file inttypes_AMOS.hh. References MIN_QUALITY. Referenced by AMOS::Sequence_t::uncompress().

void readLE (  std::istream &  in, int64_t *  i )  [inline]

Definition at line 357 of file utility_AMOS.hh. References readLE(). Referenced by main().

void readLE (  std::istream &  in, uint64_t *  i )  [inline]

Reads a little-endian 64-bit int. Parameters: in  The istream to read from i  A pointer to the int storage Precondition: Same preconditions as istream::read Returns: void Definition at line 351 of file utility_AMOS.hh. References ltoh64.

void readLE (  std::istream &  in, int32_t *  i )  [inline]

Definition at line 337 of file utility_AMOS.hh. References readLE().

void readLE (  std::istream &  in, uint32_t *  i )  [inline]

Reads a little-endian 32-bit int. Parameters: in  The istream to read from i  A pointer to the int storage Precondition: Same preconditions as istream::read Returns: void Definition at line 331 of file utility_AMOS.hh. References ltoh32.

void readLE (  std::istream &  in, int16_t *  i )  [inline]

Definition at line 317 of file utility_AMOS.hh. References readLE().

void readLE (  std::istream &  in, uint16_t *  i )  [inline]

Reads a little-endian 16-bit int. Parameters: in  The istream to read from i  A pointer to the int storage Precondition: Same preconditions as istream::read Returns: void Definition at line 311 of file utility_AMOS.hh. References ltoh16.

void readLE (  std::istream &  in, BankFlags_t *  i )  [inline]

Definition at line 296 of file utility_AMOS.hh. References readLE().

void readLE (  std::istream &  in, int8_t *  i )  [inline]

Definition at line 292 of file utility_AMOS.hh. References readLE().

void readLE (  std::istream &  in, uint8_t *  i )  [inline]

Reads a little-endian 8-bit int. Parameters: in  The istream to read from i  A pointer to the int storage Precondition: Same preconditions as istream::read Returns: void Definition at line 288 of file utility_AMOS.hh. Referenced by AMOS::Bank_t::concat(), AMOS::Bank_t::fetchBID(), AMOS::BankStream_t::ignore(), AMOS::BankStream_t::operator>>(), readLE(), AMOS::Sequence_t::readRecord(), AMOS::Scaffold_t::readRecord(), AMOS::Read_t::readRecord(), AMOS::Overlap_t::readRecord(), AMOS::Link_t::readRecord(), AMOS::Layout_t::readRecord(), AMOS::Kmer_t::readRecord(), AMOS::Index_t::readRecord(), AMOS::Group_t::readRecord(), AMOS::Fragment_t::readRecord(), AMOS::Feature_t::readRecord(), AMOS::IEdge_t::readRecord(), AMOS::Tile_t::readRecord(), AMOS::Distribution_t::readRecord(), AMOS::Contig_t::readRecord(), and AMOS::Bank_t::removeBID().

void AMOS::Reverse (  char *  str  )

Reverses the contents of a string. Parameters: str  The string to reverse Returns: void Definition at line 96 of file utility_AMOS.cc.

void AMOS::Reverse (  std::string &  str  )

Reverses the contents of a string. Simply calls the STL reverse "algorithm" but in an AMOS way Parameters: str  The string to reverse Returns: void Definition at line 89 of file utility_AMOS.cc. Referenced by AMOS::Sequence_t::getQualString(), AMOS::Contig_t::getUngappedQualString(), and ReverseComplement().

void AMOS::ReverseComplement (  char *  str  )

Takes the DNA reverse complement of an IUPAC string. Complement-able IUPAC characters are ACGTUMRWSYKVHDB, while NX*- are also acceptable but are self-complementary. Characters other than these will throw an exception. Parameters: str  The string to reverse complement Exceptions: ArgumentException_t  if invalid characters are found Returns: void Definition at line 78 of file utility_AMOS.cc. References Complement(), and Reverse().

void AMOS::ReverseComplement (  std::string &  str  )

Takes the DNA reverse complement of an IUPAC string. Complement-able IUPAC characters are ACGTUMRWSYKVHDB, while NX*- are also acceptable but are self-complementary. Characters other than these will throw an exception. Parameters: str  The string to reverse complement Exceptions: ArgumentException_t  if invalid characters are found Returns: void Definition at line 67 of file utility_AMOS.cc. References Complement(), and Reverse(). Referenced by AMOS::Sequence_t::getSeqString(), and AMOS::Contig_t::getUngappedSeqString().

void* SafeCalloc (  size_t  num, size_t  size )  [inline]

Safe calloc wrapper. Detects calloc failure and throws AMOS::AllocException_t exception instead of returning a NULL pointer. Parameters: num  Number of elements to allocate size  Number of bytes per element Postcondition: The memory is allocated Exceptions: AllocException_t  on memory exhaustion Returns: Pointer to the new memory block Definition at line 60 of file utility_AMOS.hh. References AMOS_THROW_ALLOC.

void* SafeMalloc (  size_t  size  )  [inline]

Safe malloc wrapper. Detects malloc failure and throws AMOS::AllocException_t exception instead of returning a NULL pointer. Parameters: size  Number of bytes to allocate Postcondition: The memory is allocated Exceptions: AllocException_t  on memory exhaustion Returns: Pointer to the new memory block Definition at line 81 of file utility_AMOS.hh. References AMOS_THROW_ALLOC. Referenced by AMOS::Bank_t::BankPartition_t::BankPartition_t(), and AMOS::Bank_t::concat().

void* SafeRealloc (  void *  P, size_t  size )  [inline]

Safe realloc wrapper. Detects realloc failure and throws AMOS::AllocException_t exception instead of returning a NULL pointer. This helps prevent memory leaks by preventing the original memory block from being lost when the realloc function returns NULL. Parameters: P  The memory block to re-allocate size  Number of bytes to allocate Postcondition: The memory is allocated Exceptions: AllocException_t  on memory exhaustion Returns: Pointer to the new memory block Definition at line 105 of file utility_AMOS.hh. References AMOS_THROW_ALLOC. Referenced by AMOS::Bank_t::concat(), AMOS::Sequence_t::operator=(), AMOS::Kmer_t::operator=(), AMOS::Sequence_t::readRecord(), AMOS::Kmer_t::readRecord(), AMOS::Kmer_t::setSeqString(), AMOS::Sequence_t::setSequence(), and AMOS::Sequence_t::uncompress().

char* SafeStrdup (  const char *  str  )  [inline]

Safe strdup wrapper. Detects malloc failure and throws AMOS::AllocException_t exception instead of returning a NULL pointer. Parameters: str  The string to copy Postcondition: The memory is allocated and the string is copied Exceptions: AllocException_t  on memory exhaustion Returns: Pointer to the new string copy Definition at line 126 of file utility_AMOS.hh. References AMOS_THROW_ALLOC.

void AMOS::WrapString (  std::ostream &  out, const std::string &  s, int  per )

Inserts a newline every 'per' characters when writing to stream. Definition at line 341 of file datatypes_AMOS.cc. Referenced by operator<<().

void writeLE (  std::ostream &  out, const int64_t *  i )  [inline]

Definition at line 274 of file utility_AMOS.hh. References writeLE(). Referenced by main().

void writeLE (  std::ostream &  out, const uint64_t *  i )  [inline]

Writes a 64-bit int in little-endian byte order. Parameters: out  The ostream to write to i  A pointer to the int to write Precondition: Same preconditions as ostream::write Returns: void Definition at line 268 of file utility_AMOS.hh. References htol64.

void writeLE (  std::ostream &  out, const int32_t *  i )  [inline]

Definition at line 254 of file utility_AMOS.hh. References writeLE().

void writeLE (  std::ostream &  out, const uint32_t *  i )  [inline]

Writes a 32-bit int in little-endian byte order. Parameters: out  The ostream to write to i  A pointer to the int to write Precondition: Same preconditions as ostream::write Returns: void Definition at line 248 of file utility_AMOS.hh. References htol32.

void writeLE (  std::ostream &  out, const int16_t *  i )  [inline]

Definition at line 234 of file utility_AMOS.hh. References writeLE().

void writeLE (  std::ostream &  out, const uint16_t *  i )  [inline]

Writes a 16-bit int in little-endian byte order. Parameters: out  The ostream to write to i  A pointer to the int to write Precondition: Same preconditions as ostream::write Returns: void Definition at line 228 of file utility_AMOS.hh. References htol16.

void writeLE (  std::ostream &  out, const BankFlags_t *  i )  [inline]

Definition at line 213 of file utility_AMOS.hh. References writeLE().

void writeLE (  std::ostream &  out, const int8_t *  i )  [inline]

Definition at line 209 of file utility_AMOS.hh. References writeLE().

void writeLE (  std::ostream &  out, const uint8_t *  i )  [inline]

Writes an 8-bit int in little-endian byte order. Parameters: out  The ostream to write to i  A pointer to the int to write Precondition: Same preconditions as ostream::write Returns: void Definition at line 205 of file utility_AMOS.hh. Referenced by AMOS::Bank_t::appendBID(), AMOS::Bank_t::concat(), AMOS::BankStream_t::operator<<(), AMOS::Bank_t::removeBID(), AMOS::Bank_t::replaceBID(), writeLE(), AMOS::Sequence_t::writeRecord(), AMOS::Scaffold_t::writeRecord(), AMOS::Read_t::writeRecord(), AMOS::Overlap_t::writeRecord(), AMOS::Link_t::writeRecord(), AMOS::Layout_t::writeRecord(), AMOS::Kmer_t::writeRecord(), AMOS::Index_t::writeRecord(), AMOS::Group_t::writeRecord(), AMOS::Fragment_t::writeRecord(), AMOS::Feature_t::writeRecord(), AMOS::IEdge_t::writeRecord(), AMOS::Tile_t::writeRecord(), AMOS::Distribution_t::writeRecord(), and AMOS::Contig_t::writeRecord().

---

Variable Documentation

const BankMode_t AMOS::B_READ = 0x1

protected reading mode Definition at line 35 of file Bank_AMOS.hh. Referenced by AMOS::Index_t::buildContigFeature(), AMOS::Index_t::buildContigScaffold(), AMOS::Index_t::buildReadContig(), AMOS::Index_t::buildReadLibrary(), AMOS::Index_t::buildScaffoldFeature(), AMOS::Bank_t::clean(), AMOS::Bank_t::concat(), AMOS::Bank_t::fetchBID(), AMOS::BankStream_t::ignore(), AMOS::BankStream_t::operator>>(), AMOS::Bank_t::removeBID(), AMOS::Bank_t::replaceBID(), AMOS::BankStream_t::seekg(), AMOS::Bank_t::setMode(), and AMOS::Bank_t::syncIFO().

const BankMode_t AMOS::B_SPY = 0x4

unprotected reading mode, overrides all other modes Definition at line 37 of file Bank_AMOS.hh. Referenced by AMOS::Bank_t::lockIFO(), AMOS::Bank_t::setMode(), AMOS::Bank_t::syncIFO(), AMOS::Bank_t::touchFile(), and AMOS::Bank_t::unlockIFO().

const BankMode_t AMOS::B_WRITE = 0x2

protected writing mode Definition at line 36 of file Bank_AMOS.hh. Referenced by AMOS::Bank_t::appendBID(), AMOS::Bank_t::clean(), AMOS::Bank_t::clear(), AMOS::Bank_t::close(), AMOS::Bank_t::concat(), AMOS::Bank_t::create(), AMOS::Bank_t::destroy(), AMOS::Bank_t::openPartition(), AMOS::BankStream_t::operator<<(), AMOS::Bank_t::removeBID(), AMOS::Bank_t::replaceBID(), AMOS::Bank_t::setMode(), and AMOS::Bank_t::syncIFO().

const char AMOS::E_ADD = 'A'

Definition at line 23 of file Message_AMOS.hh.

const char AMOS::E_DELETE = 'D'

Definition at line 24 of file Message_AMOS.hh.

const char AMOS::E_REPLACE = 'R'

Definition at line 25 of file Message_AMOS.hh.

const NCode_t AMOS::F_ACTION = Encode ("act")

Definition at line 28 of file Message_AMOS.hh.

const NCode_t AMOS::F_ADJACENCY = Encode ("adj")

Definition at line 29 of file Message_AMOS.hh. Referenced by AMOS::Overlap_t::readMessage(), AMOS::Link_t::readMessage(), AMOS::Overlap_t::writeMessage(), and AMOS::Link_t::writeMessage().

const NCode_t AMOS::F_AHANG = Encode ("ahg")

Definition at line 27 of file Message_AMOS.hh. Referenced by AMOS::Overlap_t::readMessage(), and AMOS::Overlap_t::writeMessage().

const NCode_t AMOS::F_BASEPOSITION = Encode ("bcp")

Definition at line 30 of file Message_AMOS.hh. Referenced by AMOS::Read_t::readMessage(), and AMOS::Read_t::writeMessage().

const NCode_t AMOS::F_BHANG = Encode ("bhg")

Definition at line 31 of file Message_AMOS.hh. Referenced by AMOS::Overlap_t::readMessage(), and AMOS::Overlap_t::writeMessage().

const NCode_t AMOS::F_BID = Encode ("bid")

Definition at line 32 of file Message_AMOS.hh.

const NCode_t AMOS::F_CLEAR = Encode ("clr")

Definition at line 33 of file Message_AMOS.hh. Referenced by AMOS::Read_t::readMessage(), AMOS::Feature_t::readMessage(), AMOS::Tile_t::readMessage(), AMOS::Read_t::writeMessage(), AMOS::Feature_t::writeMessage(), and AMOS::Tile_t::writeMessage().

const NCode_t AMOS::F_COMMENT = Encode ("com")

Definition at line 34 of file Message_AMOS.hh. Referenced by AMOS::Universal_t::readMessage(), and AMOS::Universal_t::writeMessage().

const NCode_t AMOS::F_COUNT = Encode ("cnt")

Definition at line 35 of file Message_AMOS.hh. Referenced by AMOS::Kmer_t::readMessage(), and AMOS::Kmer_t::writeMessage().

const NCode_t AMOS::F_EDGE = Encode ("edg")

Definition at line 37 of file Message_AMOS.hh. Referenced by AMOS::Scaffold_t::readMessage(), and AMOS::Scaffold_t::writeMessage().

const NCode_t AMOS::F_EID = Encode ("eid")

Definition at line 36 of file Message_AMOS.hh. Referenced by AMOS::Universal_t::readMessage(), and AMOS::Universal_t::writeMessage().

const NCode_t AMOS::F_FLAG = Encode ("flg")

Definition at line 38 of file Message_AMOS.hh. Referenced by AMOS::Universal_t::readMessage(), AMOS::Overlap_t::readMessage(), AMOS::Universal_t::writeMessage(), and AMOS::Overlap_t::writeMessage().

const NCode_t AMOS::F_FRAGMENT = Encode ("frg")

Definition at line 39 of file Message_AMOS.hh. Referenced by AMOS::Read_t::readMessage(), and AMOS::Read_t::writeMessage().

const NCode_t AMOS::F_GAPS = Encode ("gap")

Definition at line 40 of file Message_AMOS.hh. Referenced by AMOS::Tile_t::readMessage(), and AMOS::Tile_t::writeMessage().

const NCode_t AMOS::F_IID = Encode ("iid")

Definition at line 41 of file Message_AMOS.hh. Referenced by AMOS::Universal_t::readMessage(), and AMOS::Universal_t::writeMessage().

const NCode_t AMOS::F_LIBRARY = Encode ("lib")

Definition at line 42 of file Message_AMOS.hh. Referenced by AMOS::Fragment_t::readMessage(), and AMOS::Fragment_t::writeMessage().

const NCode_t AMOS::F_LINK = Encode ("lnk")

Definition at line 43 of file Message_AMOS.hh. Referenced by AMOS::IEdge_t::readMessage(), and AMOS::IEdge_t::writeMessage().

const NCode_t AMOS::F_MAP = Encode ("map")

Definition at line 44 of file Message_AMOS.hh. Referenced by AMOS::Index_t::readMessage(), AMOS::IDMap_t::readMessage(), AMOS::Index_t::writeMessage(), and AMOS::IDMap_t::writeMessage().

const NCode_t AMOS::F_MEAN = Encode ("mea")

Definition at line 45 of file Message_AMOS.hh. Referenced by AMOS::Distribution_t::readMessage(), and AMOS::Distribution_t::writeMessage().

const NCode_t AMOS::F_MEMBER = Encode ("mbr")

Definition at line 46 of file Message_AMOS.hh. Referenced by AMOS::Group_t::readMessage(), and AMOS::Group_t::writeMessage().

const NCode_t AMOS::F_NODES = Encode ("nds")

Definition at line 47 of file Message_AMOS.hh. Referenced by AMOS::Link_t::readMessage(), and AMOS::Link_t::writeMessage().

const NCode_t AMOS::F_NULL = Encode ("nul")

Definition at line 26 of file Message_AMOS.hh.

const NCode_t AMOS::F_OBJECT = Encode ("obj")

Definition at line 48 of file Message_AMOS.hh. Referenced by AMOS::Link_t::readMessage(), AMOS::Index_t::readMessage(), AMOS::IDMap_t::readMessage(), AMOS::Group_t::readMessage(), AMOS::Link_t::writeMessage(), AMOS::Index_t::writeMessage(), AMOS::IDMap_t::writeMessage(), and AMOS::Group_t::writeMessage().

const NCode_t AMOS::F_OFFSET = Encode ("off")

Definition at line 49 of file Message_AMOS.hh. Referenced by AMOS::Tile_t::readMessage(), and AMOS::Tile_t::writeMessage().

const NCode_t AMOS::F_POSITION = Encode ("pos")

Definition at line 50 of file Message_AMOS.hh. Referenced by AMOS::Read_t::readMessage(), and AMOS::Read_t::writeMessage().

const NCode_t AMOS::F_QUALITY = Encode ("qlt")

Definition at line 51 of file Message_AMOS.hh. Referenced by AMOS::Sequence_t::readMessage(), and AMOS::Sequence_t::writeMessage().

const NCode_t AMOS::F_QUALITYCLEAR = Encode ("qcr")

Definition at line 52 of file Message_AMOS.hh. Referenced by AMOS::Read_t::readMessage(), and AMOS::Read_t::writeMessage().

const NCode_t AMOS::F_READS = Encode ("rds")

Definition at line 53 of file Message_AMOS.hh. Referenced by AMOS::Overlap_t::readMessage(), AMOS::Kmer_t::readMessage(), AMOS::Fragment_t::readMessage(), AMOS::Overlap_t::writeMessage(), AMOS::Kmer_t::writeMessage(), and AMOS::Fragment_t::writeMessage().

const NCode_t AMOS::F_SCORE = Encode ("scr")

Definition at line 54 of file Message_AMOS.hh. Referenced by AMOS::Overlap_t::readMessage(), and AMOS::Overlap_t::writeMessage().

const NCode_t AMOS::F_SD = Encode ("std")

Definition at line 56 of file Message_AMOS.hh. Referenced by AMOS::Link_t::readMessage(), AMOS::Distribution_t::readMessage(), AMOS::Link_t::writeMessage(), and AMOS::Distribution_t::writeMessage().

const NCode_t AMOS::F_SEQUENCE = Encode ("seq")

Definition at line 55 of file Message_AMOS.hh. Referenced by AMOS::Sequence_t::readMessage(), AMOS::Kmer_t::readMessage(), AMOS::Sequence_t::writeMessage(), and AMOS::Kmer_t::writeMessage().

const NCode_t AMOS::F_SIZE = Encode ("sze")

Definition at line 57 of file Message_AMOS.hh. Referenced by AMOS::Link_t::readMessage(), AMOS::Index_t::readMessage(), AMOS::IDMap_t::readMessage(), AMOS::Fragment_t::readMessage(), AMOS::Link_t::writeMessage(), AMOS::Index_t::writeMessage(), AMOS::IDMap_t::writeMessage(), and AMOS::Fragment_t::writeMessage().

const NCode_t AMOS::F_SOURCE = Encode ("src")

Definition at line 58 of file Message_AMOS.hh. Referenced by AMOS::Link_t::readMessage(), AMOS::Fragment_t::readMessage(), AMOS::Feature_t::readMessage(), AMOS::Tile_t::readMessage(), AMOS::Link_t::writeMessage(), AMOS::Fragment_t::writeMessage(), AMOS::Feature_t::writeMessage(), and AMOS::Tile_t::writeMessage().

const NCode_t AMOS::F_STATUS = Encode ("sts")

Definition at line 59 of file Message_AMOS.hh. Referenced by AMOS::Universal_t::readMessage(), and AMOS::Universal_t::writeMessage().

const NCode_t AMOS::F_TYPE = Encode ("typ")

Definition at line 60 of file Message_AMOS.hh. Referenced by AMOS::Read_t::readMessage(), AMOS::Link_t::readMessage(), AMOS::Fragment_t::readMessage(), AMOS::Feature_t::readMessage(), AMOS::Read_t::writeMessage(), AMOS::Link_t::writeMessage(), AMOS::Fragment_t::writeMessage(), and AMOS::Feature_t::writeMessage().

const NCode_t AMOS::F_VECTORCLEAR = Encode ("vcr")

Definition at line 61 of file Message_AMOS.hh. Referenced by AMOS::Read_t::readMessage(), and AMOS::Read_t::writeMessage().

const NCode_t AMOS::M_CONTIG = Encode ("CTG")

Definition at line 64 of file Message_AMOS.hh.

const NCode_t AMOS::M_CONTIGEDGE = Encode ("CTE")

Definition at line 65 of file Message_AMOS.hh.

const NCode_t AMOS::M_CONTIGLINK = Encode ("CTL")

Definition at line 66 of file Message_AMOS.hh.

const NCode_t AMOS::M_DISTRIBUTION = Encode ("DST")

Definition at line 67 of file Message_AMOS.hh. Referenced by AMOS::Library_t::readMessage().

const NCode_t AMOS::M_EDGE = Encode ("EDG")

Definition at line 68 of file Message_AMOS.hh.

const NCode_t AMOS::M_FEATURE = Encode ("FEA")

Definition at line 69 of file Message_AMOS.hh.

const NCode_t AMOS::M_FRAGMENT = Encode ("FRG")

Definition at line 70 of file Message_AMOS.hh.

const NCode_t AMOS::M_GROUP = Encode ("GRP")

Definition at line 71 of file Message_AMOS.hh.

const NCode_t AMOS::M_IDMAP = Encode ("MAP")

Definition at line 76 of file Message_AMOS.hh.

const NCode_t AMOS::M_INDEX = Encode ("IDX")

Definition at line 77 of file Message_AMOS.hh.

const NCode_t AMOS::M_KMER = Encode ("KMR")

Definition at line 72 of file Message_AMOS.hh.

const NCode_t AMOS::M_LAYOUT = Encode ("LAY")

Definition at line 73 of file Message_AMOS.hh.

const NCode_t AMOS::M_LIBRARY = Encode ("LIB")

Definition at line 74 of file Message_AMOS.hh.

const NCode_t AMOS::M_LINK = Encode ("LNK")

Definition at line 75 of file Message_AMOS.hh.

const NCode_t AMOS::M_NULL = Encode ("NUL")

Definition at line 62 of file Message_AMOS.hh. Referenced by AMOS::Message_t::clear(), and AMOS::Message_t::Message_t().

const NCode_t AMOS::M_OVERLAP = Encode ("OVL")

Definition at line 78 of file Message_AMOS.hh.

const NCode_t AMOS::M_READ = Encode ("RED")

Definition at line 79 of file Message_AMOS.hh.

const NCode_t AMOS::M_SCAFFOLD = Encode ("SCF")

Definition at line 80 of file Message_AMOS.hh.

const NCode_t AMOS::M_SCAFFOLDEDGE = Encode ("SCE")

Definition at line 81 of file Message_AMOS.hh.

const NCode_t AMOS::M_SCAFFOLDLINK = Encode ("SCL")

Definition at line 82 of file Message_AMOS.hh.

const NCode_t AMOS::M_SEQUENCE = Encode ("SEQ")

Definition at line 83 of file Message_AMOS.hh.

const NCode_t AMOS::M_TILE = Encode ("TLE")

Definition at line 84 of file Message_AMOS.hh. Referenced by AMOS::Scaffold_t::readMessage(), AMOS::Layout_t::readMessage(), and AMOS::Contig_t::readMessage().

const NCode_t AMOS::M_UNIVERSAL = Encode ("UNV")

Definition at line 63 of file Message_AMOS.hh.

const ID_t AMOS::MAX_ID = ~((uint32_t)0)

(unsigned 32bit int) Definition at line 41 of file inttypes_AMOS.hh.

const Pos_t AMOS::MAX_POS = ~((uint32_t)0) >> 1

( signed 32bit int) Definition at line 43 of file inttypes_AMOS.hh. Referenced by AMOS::Scaffold_t::getSpan(), and AMOS::Layout_t::getSpan().

const char AMOS::MAX_QUALITY = '0' + 63

max quality score definition Definition at line 36 of file inttypes_AMOS.hh.

const Size_t AMOS::MAX_SIZE = ~((uint32_t)0) >> 1

( signed 32bit int) Definition at line 42 of file inttypes_AMOS.hh.

const char AMOS::MIN_QUALITY = '0'

min quality score definition Definition at line 35 of file inttypes_AMOS.hh. Referenced by Char2Qual(), and Qual2Char().

const uint8_t AMOS::NCODE_SIZE = 3

length of the NCode strings Definition at line 31 of file inttypes_AMOS.hh. Referenced by AMOS::Message_t::read(), AMOS::Link_t::readMessage(), AMOS::Index_t::readMessage(), AMOS::IDMap_t::readMessage(), AMOS::Group_t::readMessage(), AMOS::Fragment_t::readMessage(), AMOS::Feature_t::readMessage(), and AMOS::Message_t::skip().

const char AMOS::NL_CHAR = '\n'

newline char Definition at line 38 of file inttypes_AMOS.hh. Referenced by AMOS::Message_t::read(), AMOS::IBankable_t::setEID(), AMOS::Message_t::setField(), AMOS::Kmer_t::setSeqString(), AMOS::Sequence_t::setSequence(), AMOS::Message_t::skip(), AMOS::Message_t::write(), AMOS::IDMap_t::write(), AMOS::Sequence_t::writeMessage(), AMOS::Index_t::writeMessage(), and AMOS::IDMap_t::writeMessage().

const char AMOS::NULL_CHAR = '\0'

null char Definition at line 37 of file inttypes_AMOS.hh. Referenced by AMOS::Sequence_t::getQualString(), AMOS::Sequence_t::getSeqString(), AMOS::Kmer_t::getSeqString(), AMOS::Message_t::read(), AMOS::Message_t::skip(), and AMOS::Bank_t::syncIFO().

const ID_t AMOS::NULL_ID = 0

NULL ID definition. Definition at line 33 of file inttypes_AMOS.hh. Referenced by AMOS::BankStream_t::BankStream_t(), AMOS::Index_t::buildContigFeature(), AMOS::Index_t::buildContigScaffold(), AMOS::Index_t::buildReadContig(), AMOS::Index_t::buildReadLibrary(), AMOS::Index_t::buildReadMate(), AMOS::Index_t::buildScaffoldFeature(), AMOS::Read_t::clear(), AMOS::Overlap_t::clear(), AMOS::Link_t::clear(), AMOS::Fragment_t::clear(), AMOS::Feature_t::clear(), AMOS::Tile_t::clear(), AMOS::IBankable_t::clear(), AMOS::Bank_t::clear(), AMOS::Feature_t::Feature_t(), AMOS::Fragment_t::Fragment_t(), AMOS::Bank_t::getMaxIID(), AMOS::IBankable_t::IBankable_t(), AMOS::Bank_t::init(), AMOS::IDMap_t::insert(), AMOS::Link_t::Link_t(), AMOS::IDMap_t::lookupBID(), AMOS::Bank_t::lookupBID(), AMOS::IDMap_t::lookupIID(), AMOS::BankStream_t::operator>>(), AMOS::Overlap_t::Overlap_t(), AMOS::Read_t::Read_t(), AMOS::Kmer_t::readRecord(), AMOS::Group_t::readRecord(), AMOS::IEdge_t::readRecord(), AMOS::IDMap_t::remove(), AMOS::Tile_t::Tile_t(), AMOS::Universal_t::writeMessage(), AMOS::Read_t::writeMessage(), AMOS::Overlap_t::writeMessage(), AMOS::Link_t::writeMessage(), AMOS::Fragment_t::writeMessage(), AMOS::Feature_t::writeMessage(), and AMOS::Tile_t::writeMessage().

const NCode_t AMOS::NULL_NCODE = 0

NULL NCode definition. Definition at line 32 of file inttypes_AMOS.hh. Referenced by AMOS::Link_t::clear(), AMOS::Index_t::clear(), AMOS::IDMap_t::clear(), AMOS::Group_t::clear(), AMOS::Fragment_t::clear(), AMOS::Feature_t::clear(), AMOS::Feature_t::Feature_t(), AMOS::Fragment_t::Fragment_t(), AMOS::Group_t::Group_t(), AMOS::IDMap_t::IDMap_t(), AMOS::Index_t::Index_t(), AMOS::Link_t::Link_t(), AMOS::Message_t::read(), AMOS::ScaffoldLink_t::readMessage(), AMOS::ContigLink_t::readMessage(), AMOS::ScaffoldLink_t::readRecord(), AMOS::ContigLink_t::readRecord(), AMOS::Message_t::skip(), AMOS::Link_t::writeMessage(), AMOS::Index_t::writeMessage(), AMOS::IDMap_t::writeMessage(), AMOS::Group_t::writeMessage(), AMOS::Fragment_t::writeMessage(), and AMOS::Feature_t::writeMessage().

const Status_t AMOS::NULL_STATUS = 0

NULL status definition. Definition at line 34 of file inttypes_AMOS.hh. Referenced by AMOS::Universal_t::clear(), AMOS::Universal_t::Universal_t(), and AMOS::Universal_t::writeMessage().

const std::string AMOS::NULL_STRING = &NULL_CHAR

null string Definition at line 39 of file inttypes_AMOS.hh. Referenced by AMOS::Bank_t::addPartition(), AMOS::IDMap_t::insert(), AMOS::IDMap_t::lookupEID(), main(), AMOS::Universal_t::writeMessage(), AMOS::Scaffold_t::writeMessage(), AMOS::Read_t::writeMessage(), AMOS::Overlap_t::writeMessage(), AMOS::Link_t::writeMessage(), AMOS::Kmer_t::writeMessage(), AMOS::Index_t::writeMessage(), AMOS::IDMap_t::writeMessage(), AMOS::Group_t::writeMessage(), AMOS::Fragment_t::writeMessage(), AMOS::Feature_t::writeMessage(), AMOS::IEdge_t::writeMessage(), AMOS::Tile_t::writeMessage(), and AMOS::Distribution_t::writeMessage().

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