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Searched refs:CDstart (Results 1 – 12 of 12) sorted by relevance

/dports/biology/cufflinks/cufflinks-2.2.1-89-gdc3b0cb/src/
H A Dgff.cpp535 if (CDstart==0 || segstart<CDstart) CDstart=segstart; in addExon()
542 if (CDstart==0 || segstart<CDstart) { in addExon()
758 CDstart=0; in GffObj()
1566 cds_start=CDstart; in getCDS_ends()
1600 if (CDstart>=sgstart && CDstart<=sgend) { in mRNA_CDS_coords()
1627 if (CDstart>=sgstart && CDstart<=sgend) { in mRNA_CDS_coords()
1757 if (CDstart>=sgstart && CDstart<=sgend) { in getSpliced()
1786 if (CDstart>=sgstart && CDstart<=sgend) { in getSpliced()
2016 pstart=CDstart; in printGxf()
2109 if (CDstart>=sgstart && CDstart<=sgend) in getCDSegs()
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H A Dgff_utils.cpp332 if (tfrom->CDstart==0) return; in preserveContainedCDS()
333 if (t->CDstart) { in preserveContainedCDS()
334 if (tfrom->CDstart<t->CDstart && tfrom->CDstart>=t->start) in preserveContainedCDS()
335 t->CDstart=tfrom->CDstart; in preserveContainedCDS()
340 t->addCDS(tfrom->CDstart, tfrom->CDend, tfrom->CDphase); in preserveContainedCDS()
H A Dgff.h467 uint CDstart; //CDS start coord variable
579 CDstart=0; // hasCDS <=> CDstart>0
620 bool hasCDS() { return (CDstart>0); } in hasCDS()
758 if (CDstart>0) xcoordseg(CDstart, CDend);
791 if (CDstart>0) unxcoordseg(CDstart, CDend); in unxcoord()
H A Dgffread.cpp274 if ((int)gffrec.CDstart>adj) { in adjust_stopcodon()
276 gffrec.CDstart-=adj; in adjust_stopcodon()
279 if (gffrec.exons.First()->start==gffrec.CDstart+adj) { in adjust_stopcodon()
285 else if (gffrec.exons.First()->start>=gffrec.CDstart) { in adjust_stopcodon()
549 if (gffrec.CDstart>0) { in process_transcript()
661 if (wCDSonly && gffrec->CDstart==0) { in validateGffRec()
H A Dcuffcompare.cpp1161 if (c->ref==NULL || c->ref->CDstart==0) continue; //no ref or CDS available in protCluster()
/dports/biology/stringtie/stringtie-2.1.1/gclib/
H A Dgff.cpp807 this->CDstart=cd_start; in setCDS()
833 this->CDstart=cd_start; in setCDS()
964 if (CDstart==0 || CDstart>cds->start) CDstart=cds->start; in transferCDS()
1098 CDstart=0; in GffObj()
1147 CDstart=0; in GffObj()
2208 if (CDstart>=exons[i]->start && CDstart<=exons[i]->end) { in finalize()
2335 int cd_start=CDstart>0? CDstart-1 : start-1; in printBED()
2353 if (CDstart>0) BED_addAttribute(fout, numattrs,"CDS=%d:%d",CDstart-1, CDend); in printBED()
2968 pstart=CDstart; in printGxf()
3087 if (CDstart>=sgstart && CDstart<=sgend) in getCDSegs()
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H A Dgff.h732 uint CDstart; //CDS lowest coordinate variable
819 CDstart=0; // hasCDS <=> CDstart>0
856 bool hasCDS() { return (CDstart>0); } in hasCDS()
/dports/biology/libgff/libgff-2.0.0/src/
H A Dgff.cpp807 this->CDstart=cd_start; in setCDS()
833 this->CDstart=cd_start; in setCDS()
964 if (CDstart==0 || CDstart>cds->start) CDstart=cds->start; in transferCDS()
1098 CDstart=0; in GffObj()
1147 CDstart=0; in GffObj()
2208 if (CDstart>=exons[i]->start && CDstart<=exons[i]->end) { in finalize()
2335 int cd_start=CDstart>0? CDstart-1 : start-1; in printBED()
2353 if (CDstart>0) BED_addAttribute(fout, numattrs,"CDS=%d:%d",CDstart-1, CDend); in printBED()
2968 pstart=CDstart; in printGxf()
3087 if (CDstart>=sgstart && CDstart<=sgend) in getCDSegs()
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/dports/biology/gffread/gffread-0.12.7/gclib/
H A Dgff.cpp823 this->CDstart=cd_start; in setCDS()
849 this->CDstart=cd_start; in setCDS()
980 if (CDstart==0 || CDstart>cds->start) CDstart=cds->start; in transferCDS()
1114 CDstart=0; in GffObj()
1163 CDstart=0; in GffObj()
2224 if (CDstart>=exons[i]->start && CDstart<=exons[i]->end) { in finalize()
2354 int cd_start=CDstart>0? CDstart-1 : start-1; in printBED()
2372 if (CDstart>0) BED_addAttribute(fout, numattrs,"CDS=%d:%d",CDstart-1, CDend); in printBED()
3013 pstart=CDstart; in printGxf()
3119 if (CDstart>=sgstart && CDstart<=sgend) in getCDSegs()
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H A Dgff.h749 uint CDstart; //CDS lowest coordinate variable
836 CDstart=0; // hasCDS <=> CDstart>0
871 bool hasCDS() { return (CDstart>0); } in hasCDS()
/dports/biology/gffread/gffread-0.12.7/
H A Dgff_utils.cpp256 if ((int)gffrec.CDstart>adj) { in adjust_stopcodon()
257 gffrec.CDstart-=adj; in adjust_stopcodon()
259 if (gffrec.exons.First()->start>gffrec.CDstart) { in adjust_stopcodon()
260 gffrec.covlen+=gffrec.exons.First()->start - gffrec.CDstart; in adjust_stopcodon()
261 gffrec.exons.First()->start=gffrec.CDstart; in adjust_stopcodon()
262 gffrec.start=gffrec.CDstart; in adjust_stopcodon()
465 if (wCDSonly && gffrec->CDstart==0) { in checkFilters()
657 if (gffrec.strand=='-') gffrec.CDstart=gc; in process_transcript()
795 if (!wfaNoCDS && gffrec.CDstart>0) { in process_transcript()
/dports/biology/libgff/libgff-2.0.0/include/
H A Dgff.h732 uint CDstart; //CDS lowest coordinate variable
819 CDstart=0; // hasCDS <=> CDstart>0
856 bool hasCDS() { return (CDstart>0); } in hasCDS()