9171b3f661fe87a3bc4f3e02c0593699510cc152
markd
  Wed Jun 24 05:49:12 2015 -0700
add option to gtfToGenePred to include gene and transcript version number that now part of their GTF files in the gene/transcripts ids (no redmine)

diff --git src/inc/gff.h src/inc/gff.h
index 15f7c3d..03b035d 100644
--- src/inc/gff.h
+++ src/inc/gff.h
@@ -17,30 +17,33 @@
     char *feature;  /* Type field. (Intron, CDS, etc). Not allocated here. */
     int start;      /* Start of feature in sequence. Starts with 0, not 1 */
     int end;        /* End of feature in sequence. End is not included. */
     double score;   /* Score. */
     char strand;    /* Strand of sequence feature is on. + or - or .*/
     char frame;     /* Frame feature is in. 1, 2, 3, or . */
     char *group;    /* Group line is in. Not allocated here.  Corresponds to transcript_id in GTF */
     char *geneId;    /* gene_id in GTF, NULL in GFF.  Not allocated here. */
     char *exonId;       /* exon_id in GTF, NULL in GFF. Not allocated here. */
     int exonNumber; /* O in GFF or if missing in GTF.  Otherwise exon number. */
     char *intronId;       /* intron_id in GTF, NULL in GFF. Not allocated here. */
     char *intronStatus;   /* intron status. Not allocated here. */
     char *proteinId;      /* protein_id in GTF, NULL in GFF. Not allocated here. */
     char *geneName;       /* gene_name or NULL in GTF, NULL in GFF. Not allocated here. */
     char *transcriptName; /* transcript_name or NULL in GTF, NULL in GFF. Not allocated here. */
+    char *geneVersion;  /* gene_version or NULL or NULL in GTF, NULL in GFF. Not allocated here. */
+    char *transcriptVersion;  /* transcript_version or NULL or NULL in GTF, NULL in GFF. Not allocated here. */
+    char *proteinVersion;  /* protein_version or NULL or NULL in GTF, NULL in GFF. Not allocated here. */
     };
 
 struct gffGroup
 /* A group of lines in a GFF file (all that share the same group field). */
     {
     struct gffGroup *next;   /* Next group in file. */
     char *name;     /* Name of group. Not allocated here. */
     char *seq;      /* Name of sequence. Not allocated here. */
     char *source;      /* Name of source program. Not allocated here. */
     /* The next three fields are only valid after call to gffGroupLines() */
     int start;      /* Start of feature in sequence. Starts with 0, not 1 */
     int end;        /* End of feature in sequence. End is not included. */
     char strand;    /* Strand of sequence. */
     struct gffLine *lineList;  /* List of lines in group. */
     };