179 BEDLine::BEDLine(GffReader* reader, const char* l): skip(true), dupline(NULL), line(NULL), llen(0),  in BEDLine()
397 GffLine::GffLine(GffReader* reader, const char* l): _parents(NULL), _parents_len(0),  in GffLine()
867 int GffObj::readExon(GffReader& reader, GffLine& gl) {  in readExon()
1107 GffObj::GffObj(GffReader& gfrd, BEDLine& bedline):GSeg(0,0),  in GffObj()
1156 GffObj::GffObj(GffReader &gfrd, GffLine& gffline):  in GffObj()
1296 BEDLine* GffReader::nextBEDLine() {  in nextBEDLine()
1317 GffLine* GffReader::nextGffLine() {  in nextGffLine()
1359 char* GffReader::gfoBuildId(const char* id, const char* ctg) {  in gfoBuildId()
1370 GffObj* GffReader::gfoAdd(GffObj* gfo) {  in gfoAdd()
1379 GffObj* GffReader::gfoAdd(GPVec<GffObj>& glst, GffObj* gfo) {  in gfoAdd()
1384 GffObj* GffReader::gfoReplace(GPVec<GffObj>& glst, GffObj* gfo, GffObj* toreplace) {  in gfoReplace()
1395 bool GffReader::pFind(const char* id, GPVec<GffObj>*& glst) {  in pFind()
1400 GffObj* GffReader::gfoFind(const char* id, GPVec<GffObj>*& glst,  in gfoFind()
1431 GffObj* GffReader::updateParent(GffObj* newgfo, GffObj* parent) {  in updateParent()
1447 GffObj* GffReader::newGffRec(GffLine* gffline, GffObj* parent, GffExon* pexon, GPVec<GffObj>* glst,…  in newGffRec()
1471 GffObj* GffReader::newGffRec(BEDLine* bedline, GPVec<GffObj>* glst) {  in newGffRec()
1479 GffObj* GffReader::updateGffRec(GffObj* prevgfo, GffLine* gffline) {  in updateGffRec()
1498 bool GffReader::readExonFeature(GffObj* prevgfo, GffLine* gffline, GHash<CNonExon*>* pex) {  in readExonFeature()
1530 CNonExon* GffReader::subfPoolCheck(GffLine* gffline, GHash<CNonExon*>& pex, char*& subp_name) {  in subfPoolCheck()
1545 void GffReader::subfPoolAdd(GHash<CNonExon*>& pex, GffObj* newgfo) {  in subfPoolAdd()
1554 GffObj* GffReader::promoteFeature(CNonExon* subp, char*& subp_name, GHash<CNonExon*>& pex) {  in promoteFeature()
1567 GffObj* GffReader::readNext() { //user must free the returned GffObj*  in readNext()
1640 void GffReader::readAll() {  in readAll()
1851 void GfList::finalize(GffReader* gfr) { //if set, enforce sort by locus  in finalize()
1979 bool GffObj::processGeneSegments(GffReader* gfr) {  in processGeneSegments()
2061 GffObj* GffObj::finalize(GffReader* gfr) {  in finalize()