0362494184981193a406895a488aee5e92ece803 markd Tue Feb 7 14:24:25 2023 -0800 support for converting HPRC GFF3 files from Ensembl. Not perfect, however, all genes get converted, so this can be fixed in post-preocessing diff --git src/inc/gff3.h src/inc/gff3.h index 9c15ed1..f7f0fa6 100644 --- src/inc/gff3.h +++ src/inc/gff3.h @@ -206,33 +206,40 @@ extern char *gff3AttrID; extern char *gff3AttrName; extern char *gff3AttrAlias; extern char *gff3AttrParent; extern char *gff3AttrTarget; extern char *gff3AttrGap; extern char *gff3AttrDerivesFrom; extern char *gff3AttrNote; extern char *gff3AttrDbxref; extern char *gff3AttrOntologyTerm; /* commonly used features names */ extern char *gff3FeatGene; extern char *gff3FeatPseudogene; extern char *gff3FeatMRna; +extern char *gff3FeatNCRnaGene; extern char *gff3FeatNCRna; extern char *gff3FeatRRna; extern char *gff3FeatTRna; +extern char *gff3FeatLncRna; +extern char *gff3FeatPseudogenicTranscript; +extern char *gff3FeatScRna; +extern char *gff3FeatSnRna; +extern char *gff3FeatSnoRna; +extern char *gff3FeatUnconfirmedTranscript; extern char *gff3FeatExon; extern char *gff3FeatCDS; extern char *gff3FeatThreePrimeUTR; extern char *gff3FeatFivePrimeUTR; extern char *gff3FeatStartCodon; extern char *gff3FeatStopCodon; extern char *gff3FeatTranscript; extern char *gff3FeatPrimaryTranscript; extern char *gff3FeatCGeneSegment; extern char *gff3FeatDGeneSegment; extern char *gff3FeatJGeneSegment; extern char *gff3FeatVGeneSegment; struct gff3File *gff3FileOpen(char *fileName, int maxErr, unsigned flags, FILE *errFh);