libStatGen Software 1
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Public Member Functions | |
bool | Open (const String &filename) |
void | OpenStub () |
bool | Create (const String &filename) |
bool | isOpen () |
void | Close () |
void | Rewind () |
bool | NextSection () |
bool | NextEntry () |
bool | NextBaseEntry () |
void | BeginSection (const String §ionLabel, int sectionLength) |
void | EndSection () |
void | WriteEntry (int outputPosition) |
char | GetReference (int position, char defaultBase) |
int | GetDepth (int position) |
const double * | GetLikelihoods (int position) |
const unsigned char * | GetLogLikelihoods (int position) |
int | GetMapQuality (int position) |
Static Public Member Functions | |
static const double * | GetDefaultLikelihoods () |
static const unsigned char * | GetDefaultLogLikelihoods () |
static int | GenotypeIndex (int base1, int base2) |
Public Attributes | |
bool | isStub |
IFILE | handle |
String | header |
String | label |
int | sections |
int | currentSection |
int | maxPosition |
bool | endOfSection |
glfEntry | data |
int | position |
double | likelihoods [10] |
String | indelSequence [2] |
const char * | errorMsg |
Definition at line 72 of file glfHandler.h.
glfHandler::glfHandler | ( | ) |
Definition at line 26 of file glfHandler.cpp.
glfHandler::~glfHandler | ( | ) |
Definition at line 34 of file glfHandler.cpp.
void glfHandler::BeginSection | ( | const String & | sectionLabel, |
int | sectionLength | ||
) |
Definition at line 355 of file glfHandler.cpp.
void glfHandler::Close | ( | ) |
Definition at line 147 of file glfHandler.cpp.
bool glfHandler::Create | ( | const String & | filename | ) |
Definition at line 71 of file glfHandler.cpp.
void glfHandler::EndSection | ( | ) |
Definition at line 367 of file glfHandler.cpp.
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inlinestatic |
Definition at line 132 of file glfHandler.h.
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inlinestatic |
Definition at line 123 of file glfHandler.h.
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inlinestatic |
Definition at line 127 of file glfHandler.h.
int glfHandler::GetDepth | ( | int | position | ) |
Definition at line 327 of file glfHandler.cpp.
const double * glfHandler::GetLikelihoods | ( | int | position | ) |
Definition at line 303 of file glfHandler.cpp.
const unsigned char * glfHandler::GetLogLikelihoods | ( | int | position | ) |
Definition at line 311 of file glfHandler.cpp.
int glfHandler::GetMapQuality | ( | int | position | ) |
Definition at line 335 of file glfHandler.cpp.
char glfHandler::GetReference | ( | int | position, |
char | defaultBase | ||
) |
Definition at line 319 of file glfHandler.cpp.
bool glfHandler::isOpen | ( | ) |
Definition at line 88 of file glfHandler.cpp.
bool glfHandler::NextBaseEntry | ( | ) |
Definition at line 200 of file glfHandler.cpp.
bool glfHandler::NextEntry | ( | ) |
Definition at line 214 of file glfHandler.cpp.
bool glfHandler::NextSection | ( | ) |
Definition at line 166 of file glfHandler.cpp.
bool glfHandler::Open | ( | const String & | filename | ) |
Definition at line 41 of file glfHandler.cpp.
void glfHandler::OpenStub | ( | ) |
Definition at line 60 of file glfHandler.cpp.
void glfHandler::Rewind | ( | ) |
Definition at line 153 of file glfHandler.cpp.
void glfHandler::WriteEntry | ( | int | outputPosition | ) |
Definition at line 374 of file glfHandler.cpp.
int glfHandler::currentSection |
Definition at line 83 of file glfHandler.h.
glfEntry glfHandler::data |
Definition at line 90 of file glfHandler.h.
bool glfHandler::endOfSection |
Definition at line 87 of file glfHandler.h.
const char* glfHandler::errorMsg |
Definition at line 96 of file glfHandler.h.
IFILE glfHandler::handle |
Definition at line 77 of file glfHandler.h.
String glfHandler::header |
Definition at line 78 of file glfHandler.h.
String glfHandler::indelSequence[2] |
Definition at line 93 of file glfHandler.h.
bool glfHandler::isStub |
Definition at line 76 of file glfHandler.h.
String glfHandler::label |
Definition at line 81 of file glfHandler.h.
double glfHandler::likelihoods[10] |
Definition at line 92 of file glfHandler.h.
int glfHandler::maxPosition |
Definition at line 84 of file glfHandler.h.
int glfHandler::position |
Definition at line 91 of file glfHandler.h.
int glfHandler::sections |
Definition at line 82 of file glfHandler.h.