785731775908bbc9d7f0449772ca0f42a1e669fa
braney
  Fri Apr 17 07:48:25 2015 -0700
add a few new feature types to the processing of gff3ToGenePred (rRNA,
ncRNA, primary-transcript)

diff --git src/lib/gff3.c src/lib/gff3.c
index f32a90a..154958c 100644
--- src/lib/gff3.c
+++ src/lib/gff3.c
@@ -33,38 +33,41 @@
 /* standard attribute names */
 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 *gff3FeatNCRna ="ncRNA";
+char *gff3FeatRRna = "rRNA";
 char *gff3FeatMRna = "mRNA";
 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";
 
 static bool gff3FileStopDueToErrors(struct gff3File *g3f)
 /* determine if we should stop due to the number of errors */
 {
 return g3f->errCnt > g3f->maxErr;
 }
 
 static void gff3FileErr(struct gff3File *g3f, char *format, ...)
 #if defined(__GNUC__)
 __attribute__((format(printf, 2, 3)))
 #endif
 ;
 
 static void gff3AnnErr(struct gff3Ann *g3a, char *format, ...)
 #if defined(__GNUC__)