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root/gclib/gclib/gff.cpp
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# Line 572 | Line 572
572             } //check for overlap
573     // --- no overlap, or accepted micro-overlap (ribosomal slippage)
574     // create & add the new segment
575 +   /*
576 +   if (start>0 && exontype==exgffCDS && exons.Count()==0) {
577 +      //adding a CDS directly as the first subfeature of a declared parent
578 +      segstart=start;
579 +      segend=end;
580 +      }
581 +   */
582     GffExon* enew=new GffExon(segstart, segend, sc, fr, qs, qe, exontype);
583     int eidx=exons.Add(enew);
584     if (eidx<0) {
# Line 584 | Line 591
591       return -1;            
592       }
593     covlen+=(int)(exons[eidx]->end-exons[eidx]->start)+1;
594 <   start=exons.First()->start;
595 <   end=exons.Last()->end;
594 >   if (start==0) {
595 >     start=exons.First()->start;
596 >     end=exons.Last()->end;
597 >     }
598     if (uptr!=NULL) { //collect stats about the underlying genomic sequence
599         GSeqStat* gsd=(GSeqStat*)uptr;
600         if (start<gsd->mincoord) gsd->mincoord=start;

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