Searched refs:CDstart (Results 1 – 12 of 12) sorted by relevance
/dports/biology/cufflinks/cufflinks-2.2.1-89-gdc3b0cb/src/ |
H A D | gff.cpp | 535 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() [all …]
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H A D | gff_utils.cpp | 332 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()
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H A D | gff.h | 467 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()
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H A D | gffread.cpp | 274 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()
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H A D | cuffcompare.cpp | 1161 if (c->ref==NULL || c->ref->CDstart==0) continue; //no ref or CDS available in protCluster()
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/dports/biology/stringtie/stringtie-2.1.1/gclib/ |
H A D | gff.cpp | 807 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() [all …]
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H A D | gff.h | 732 uint CDstart; //CDS lowest coordinate variable 819 CDstart=0; // hasCDS <=> CDstart>0 856 bool hasCDS() { return (CDstart>0); } in hasCDS()
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/dports/biology/libgff/libgff-2.0.0/src/ |
H A D | gff.cpp | 807 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() [all …]
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/dports/biology/gffread/gffread-0.12.7/gclib/ |
H A D | gff.cpp | 823 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() [all …]
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H A D | gff.h | 749 uint CDstart; //CDS lowest coordinate variable 836 CDstart=0; // hasCDS <=> CDstart>0 871 bool hasCDS() { return (CDstart>0); } in hasCDS()
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/dports/biology/gffread/gffread-0.12.7/ |
H A D | gff_utils.cpp | 256 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()
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/dports/biology/libgff/libgff-2.0.0/include/ |
H A D | gff.h | 732 uint CDstart; //CDS lowest coordinate variable 819 CDstart=0; // hasCDS <=> CDstart>0 856 bool hasCDS() { return (CDstart>0); } in hasCDS()
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