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/lib/gff3.c src/lib/gff3.c
index b5388dd..9c12e32 100644
--- src/lib/gff3.c
+++ src/lib/gff3.c
@@ -34,34 +34,41 @@
 char *gff3AttrID = "ID";
 char *gff3AttrName = "Name";
 char *gff3AttrAlias = "Alias";
 char *gff3AttrParent = "Parent";
 char *gff3AttrTarget = "Target";
 char *gff3AttrGap = "Gap";
 char *gff3AttrDerivesFrom = "Derives_from";
 char *gff3AttrNote = "Note";
 char *gff3AttrDbxref = "Dbxref";
 char *gff3AttrOntologyTerm = "Ontology_term";
 char *gff3AttrIsCircular = "Is_circular";
 
 /* commonly used features names */
 char *gff3FeatGene = "gene";
 char *gff3FeatPseudogene = "pseudogene";
+char *gff3FeatNCRnaGene ="ncRNA_gene";
 char *gff3FeatNCRna ="ncRNA";
 char *gff3FeatRRna = "rRNA";
 char *gff3FeatTRna = "tRNA";
 char *gff3FeatMRna = "mRNA";
+char *gff3FeatLncRna = "lnc_RNA";
+char *gff3FeatPseudogenicTranscript = "pseudogenic_transcript";
+char *gff3FeatScRna = "scRNA";
+char *gff3FeatSnRna = "snRNA";
+char *gff3FeatSnoRna = "snoRNA";
+char *gff3FeatUnconfirmedTranscript = "unconfirmed_transcript";
 char *gff3FeatExon = "exon";
 char *gff3FeatCDS = "CDS";
 char *gff3FeatThreePrimeUTR = "three_prime_UTR";
 char *gff3FeatFivePrimeUTR = "five_prime_UTR";
 char *gff3FeatStartCodon = "start_codon";
 char *gff3FeatStopCodon = "stop_codon";
 char *gff3FeatTranscript = "transcript";
 char *gff3FeatPrimaryTranscript = "primary_transcript";
 char *gff3FeatCGeneSegment = "C_gene_segment";
 char *gff3FeatDGeneSegment = "D_gene_segment";
 char *gff3FeatJGeneSegment = "J_gene_segment";
 char *gff3FeatVGeneSegment = "V_gene_segment";
 
 static bool gff3FileStopDueToErrors(struct gff3File *g3f)
 /* determine if we should stop due to the number of errors */