| /dports/biology/cufflinks/cufflinks-2.2.1-89-gdc3b0cb/src/ |
| H A D | gff.h | 66 class GffReader; variable
111 GffLine(GffReader* reader, const char* l); //parse the line accordingly
449 friend class GffReader; variable
534 int addExon(GffReader* reader, GffLine* gl, bool keepAttr=false, bool noExonAttr=true);
550 GffObj(GffReader* gfrd, GffLine* gffline, bool keepAttrs=false, bool noExonAttr=true);
603 GffObj* finalize(GffReader* gfr, bool mergeCloseExons=false,
945 void finalize(GffReader* gfr, bool mergeCloseExons,
998 class GffReader {
1041 GffReader(FILE* f=NULL, bool t_only=false, bool sortbyloc=false):discarded_ids(true), in discarded_ids()
1061 GffReader(char* fn, bool t_only=false, bool sort=false):discarded_ids(true), phash(true), in discarded_ids()
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| H A D | gff.cpp | 865 GffLine* GffReader::nextGffLine() { in nextGffLine()
899 char* GffReader::gfoBuildId(const char* id, const char* ctg) { in gfoBuildId()
916 GffObj* GffReader::gfoAdd(GffObj* gfo) { in gfoAdd()
926 GffObj* GffReader::gfoAdd(GPVec<GffObj>& glst, GffObj* gfo) { in gfoAdd()
931 bool GffReader::pFind(const char* id, GPVec<GffObj>*& glst) { in pFind()
936 GffObj* GffReader::gfoFind(const char* id, GPVec<GffObj>*& glst, in gfoFind()
981 GffObj* GffReader::updateParent(GffObj* newgfo, GffObj* parent) { in updateParent()
997 GffObj* GffReader::newGffRec(GffLine* gffline, bool keepAttr, bool noExonAttr, in newGffRec()
1023 GffObj* GffReader::updateGffRec(GffObj* prevgfo, GffLine* gffline, in updateGffRec()
1085 void GffReader::subfPoolAdd(GHash<CNonExon>& pex, GffObj* newgfo) { in subfPoolAdd()
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| H A D | gtf_tracking.cpp | 596 GffReader gffr(f, true); //loading only recognizable transcript features in read_transcripts()
628 GffReader* gffr=new GffReader(f, true); //load only transcript annotations in read_mRNAs()
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| H A D | gff_utils.cpp | 573 …GffReader* gffr=new GffReader(f, this->transcriptsOnly, false); //not only mRNA features, not sort… in load()
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| /dports/biology/stringtie/stringtie-2.1.1/gclib/ |
| H A D | gff.h | 55 class GffReader; variable
194 BEDLine(GffReader* r=NULL, const char* l=NULL);
254 GffLine(GffReader* reader, const char* l); //parse the line accordingly
713 friend class GffReader; variable
773 int readExon(GffReader& reader, GffLine& gl);
795 GffObj(GffReader& gfrd, BEDLine& bedline);
796 GffObj(GffReader& gfrd, GffLine& gffline);
839 GffObj* finalize(GffReader* gfr);
1094 void finalize(GffReader* gfr);
1137 class GffReader {
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| H A D | gff.cpp | 851 int GffObj::readExon(GffReader& reader, GffLine& gl) { in readExon()
1091 GffObj::GffObj(GffReader& gfrd, BEDLine& bedline):GSeg(0,0), in GffObj()
1140 GffObj::GffObj(GffReader &gfrd, GffLine& gffline): in GffObj()
1279 BEDLine* GffReader::nextBEDLine() { in nextBEDLine()
1300 GffLine* GffReader::nextGffLine() { in nextGffLine()
1353 GffObj* GffReader::gfoAdd(GffObj* gfo) { in gfoAdd()
1362 GffObj* GffReader::gfoAdd(GPVec<GffObj>& glst, GffObj* gfo) { in gfoAdd()
1378 bool GffReader::pFind(const char* id, GPVec<GffObj>*& glst) { in pFind()
1624 void GffReader::readAll() { in readAll()
1963 bool GffObj::processGeneSegments(GffReader* gfr) { in processGeneSegments()
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| /dports/biology/libgff/libgff-2.0.0/include/ |
| H A D | gff.h | 55 class GffReader; variable
194 BEDLine(GffReader* r=NULL, const char* l=NULL);
254 GffLine(GffReader* reader, const char* l); //parse the line accordingly
713 friend class GffReader; variable
773 int readExon(GffReader& reader, GffLine& gl);
795 GffObj(GffReader& gfrd, BEDLine& bedline);
796 GffObj(GffReader& gfrd, GffLine& gffline);
839 GffObj* finalize(GffReader* gfr);
1094 void finalize(GffReader* gfr);
1137 class GffReader {
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| /dports/biology/gffread/gffread-0.12.7/gclib/ |
| H A D | gff.h | 56 class GffReader; variable
208 BEDLine(GffReader* r=NULL, const char* l=NULL);
268 GffLine(GffReader* reader, const char* l); //parse the line accordingly
730 friend class GffReader; variable
790 int readExon(GffReader& reader, GffLine& gl);
812 GffObj(GffReader& gfrd, BEDLine& bedline);
813 GffObj(GffReader& gfrd, GffLine& gffline);
856 GffObj* finalize(GffReader* gfr);
1111 void finalize(GffReader* gfr);
1154 class GffReader {
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| H A D | gff.cpp | 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()
1370 GffObj* GffReader::gfoAdd(GffObj* gfo) { in gfoAdd()
1379 GffObj* GffReader::gfoAdd(GPVec<GffObj>& glst, GffObj* gfo) { in gfoAdd()
1395 bool GffReader::pFind(const char* id, GPVec<GffObj>*& glst) { in pFind()
1640 void GffReader::readAll() { in readAll()
1979 bool GffObj::processGeneSegments(GffReader* gfr) { in processGeneSegments()
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| /dports/biology/libgff/libgff-2.0.0/src/ |
| H A D | gff.cpp | 851 int GffObj::readExon(GffReader& reader, GffLine& gl) { in readExon()
1091 GffObj::GffObj(GffReader& gfrd, BEDLine& bedline):GSeg(0,0), in GffObj()
1140 GffObj::GffObj(GffReader &gfrd, GffLine& gffline): in GffObj()
1279 BEDLine* GffReader::nextBEDLine() { in nextBEDLine()
1300 GffLine* GffReader::nextGffLine() { in nextGffLine()
1353 GffObj* GffReader::gfoAdd(GffObj* gfo) { in gfoAdd()
1362 GffObj* GffReader::gfoAdd(GPVec<GffObj>& glst, GffObj* gfo) { in gfoAdd()
1378 bool GffReader::pFind(const char* id, GPVec<GffObj>*& glst) { in pFind()
1624 void GffReader::readAll() { in readAll()
1963 bool GffObj::processGeneSegments(GffReader* gfr) { in processGeneSegments()
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| H A D | TestGFFParse.cpp | 14 GffReader reader(argv[1], true, false); in main()
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| /dports/biology/stringtie/stringtie-2.1.1/ |
| H A D | tmerge.cpp | 31 GffReader gfr(gtf.chars(), true, true); //transcript only, sorted by location in convert2BAM()
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| H A D | rlink.h | 62 void add(GffReader* gffr, GffObj* t) { in add()
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| H A D | stringtie.cpp | 305 GffReader gffr(f, true, true); //loading only recognizable transcript features in main()
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| /dports/biology/gffread/gffread-0.12.7/ |
| H A D | gff_utils.cpp | 1437 GffReader* gffr=new GffReader(f, this->transcriptsOnly, true); //not only mRNA features, sorted in load()
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