#include <inttypes.h>
#include <limits.h>
#include <string>
Include dependency graph for inttypes_AMOS.hh:
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Namespaces | |
namespace | AMOS |
Classes | |
struct | AMOS::BankFlags_t |
8 bit flag set for IBankable types More... | |
Defines | |
#define | __inttypes_AMOS_HH 1 |
ints of the form [u]int(size)_t, i.e. int32_t | |
#define | swap16(x) ((((x) >> 8) & 0xff) | (((x) & 0xff) << 8)) |
swaps the bytes in a 16-bit value | |
#define | swap32(x) |
swaps the bytes in a 32-bit value | |
#define | swap64(x) |
swaps the bytes in a 64-bit value | |
#define | htol16(x) (x) |
host to little-endian 16-bits | |
#define | htol32(x) (x) |
host to little-endian 32-bits | |
#define | htol64(x) (x) |
host to little-endian 64-bits | |
#define | ltoh16(x) (x) |
little-endian to host 16-bits | |
#define | ltoh32(x) (x) |
little-endian to host 32-bits | |
#define | ltoh64(x) (x) |
little-endian to host 64-bits | |
#define | htob16(x) swap16(x) |
host to big-endian 16-bits | |
#define | htob32(x) swap32(x) |
host to big-endian 32-bits | |
#define | htob64(x) swap64(x) |
host to big-endian 64-bits | |
#define | btoh16(x) swap16(x) |
big-endian to host 16-bits | |
#define | btoh32(x) swap32(x) |
big-endian to host 32-bits | |
#define | btoh64(x) swap64(x) |
big-endian to host 64-bits | |
Typedefs | |
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 | |
Functions | |
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. | |
Variables | |
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) |
Definition in file inttypes_AMOS.hh.
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ints of the form [u]int(size)_t, i.e. int32_t Definition at line 11 of file inttypes_AMOS.hh. |
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big-endian to host 16-bits Definition at line 216 of file inttypes_AMOS.hh. |
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big-endian to host 32-bits Definition at line 217 of file inttypes_AMOS.hh. |
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big-endian to host 64-bits Definition at line 218 of file inttypes_AMOS.hh. |
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host to big-endian 16-bits Definition at line 213 of file inttypes_AMOS.hh. |
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host to big-endian 32-bits Definition at line 214 of file inttypes_AMOS.hh. |
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host to big-endian 64-bits Definition at line 215 of file inttypes_AMOS.hh. |
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host to little-endian 16-bits Definition at line 196 of file inttypes_AMOS.hh. Referenced by AMOS::writeLE(). |
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host to little-endian 32-bits Definition at line 197 of file inttypes_AMOS.hh. Referenced by AMOS::writeLE(). |
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host to little-endian 64-bits Definition at line 198 of file inttypes_AMOS.hh. Referenced by AMOS::writeLE(). |
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little-endian to host 16-bits Definition at line 199 of file inttypes_AMOS.hh. Referenced by AMOS::readLE(). |
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little-endian to host 32-bits Definition at line 200 of file inttypes_AMOS.hh. Referenced by AMOS::readLE(). |
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little-endian to host 64-bits Definition at line 201 of file inttypes_AMOS.hh. Referenced by AMOS::readLE(). |
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swaps the bytes in a 16-bit value Definition at line 152 of file inttypes_AMOS.hh. |
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Value: swaps the bytes in a 32-bit value Definition at line 158 of file inttypes_AMOS.hh. |
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Value: swaps the bytes in a 64-bit value Definition at line 166 of file inttypes_AMOS.hh. |
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standard deviation type Definition at line 26 of file inttypes_AMOS.hh. Referenced by AMOS::Link_t::getSD(), and AMOS::Link_t::setSD(). |
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status type Definition at line 29 of file inttypes_AMOS.hh. Referenced by AMOS::Universal_t::getStatus(), and AMOS::Universal_t::setStatus(). |
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Converts a printable quality character to an int.
References AMOS::MIN_QUALITY. Referenced by AMOS::Sequence_t::compress(). |
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Converts an NCode integer to an AMOS message/field type.
References AMOS::NCode_t. Referenced by AMOS::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(). |
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Converts an AMOS message/field type to an NCode integer.
References AMOS::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(). |
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Converts a quality int into a printable character.
References AMOS::MIN_QUALITY. Referenced by AMOS::Sequence_t::uncompress(). |
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(unsigned 32bit int) Definition at line 41 of file inttypes_AMOS.hh. |
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( signed 32bit int) Definition at line 43 of file inttypes_AMOS.hh. Referenced by AMOS::Scaffold_t::getSpan(), and AMOS::Layout_t::getSpan(). |
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max quality score definition Definition at line 36 of file inttypes_AMOS.hh. |
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( signed 32bit int) Definition at line 42 of file inttypes_AMOS.hh. |
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min quality score definition Definition at line 35 of file inttypes_AMOS.hh. Referenced by AMOS::Char2Qual(), and AMOS::Qual2Char(). |
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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(). |
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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(). |
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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(). |
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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(). |
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