fdef579bae3c23fe4057b74062858bcd60a79209 markd Mon Apr 18 14:42:07 2016 -0700 removed accidently checked in garbage diff --git src/hg/genePredToGtf/genePredToGtf.c src/hg/genePredToGtf/genePredToGtf.c index a900d67..b0bf513 100644 --- src/hg/genePredToGtf/genePredToGtf.c +++ src/hg/genePredToGtf/genePredToGtf.c @@ -345,31 +345,31 @@ } if (utr && (exonEnd > lastUtrStart)) { int start = max(lastUtrStart, exonStart); writeGtfLine(f, source, name, geneName, chrom, strand, ((strand == '+') ? "3UTR" : "5UTR"), start, exonEnd, i, -1); } } void genePredWriteToGtf(struct genePred *gp, char *source, struct hash *dupeHash, FILE *f) /* Write out genePredName to GTF file. */ { int i; -mv old/char *name = findUniqueName(dupeHash, gp->name); +char *name = findUniqueName(dupeHash, gp->name); char *geneName = gp->name2; char *chrom = gp->chrom; char strand = gp->strand[0]; int *frames = (gp->optFields & genePredExonFramesFld) ? gp->exonFrames : calcFrames(gp); struct codonCoords firstCodon = findFirstCodon(gp, frames); struct codonCoords lastCodon = findLastCodon(gp, frames); // figure out bounds of CDS and UTR regions, moving stop codon to outside of // CDS. int firstUtrEnd = gp->cdsStart, lastUtrStart = gp->cdsEnd; int cdsStart = gp->cdsStart, cdsEnd = gp->cdsEnd; if ((strand == '+') && codonComplete(&lastCodon)) cdsEnd = movePos(gp, lastUtrStart, -3); if ((strand == '-') && codonComplete(&firstCodon)) cdsStart = movePos(gp, cdsStart, 3);