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/hg/inc/genePred.h src/hg/inc/genePred.h
index b2462e3..71dd402 100644
--- src/hg/inc/genePred.h
+++ src/hg/inc/genePred.h
@@ -37,32 +37,34 @@
 
 enum genePredFromPslOpts
 /* bit set of options for genePredFromPsl3 */
 {
     genePredPslDefaults = 0x00,  /* used if nothing special */
     genePredPslCdsMod3  = 0x01   /* only merge gaps in CDS if mod 3 */
 };
 
 
 enum genePredFromGxfOpts
 /* bit set of options for genePredFromGroupedGff/genePredFromGroupedGtf */
 {
     genePredGxfDefaults = 0x00,            /* used if nothing special */
     genePredGxfImpliedStopAfterCds = 0x01, /* stop codon is implied outside of
                                             * the annotated CDS bounds  */
-    genePredGxfGeneNameAsName2 = 0x02      /* use gene_name instead of gene_id
+    genePredGxfGeneNameAsName2 = 0x02,     /* use gene_name instead of gene_id
                                             * for name2 */
+    genePredGxfIncludeVersion = 0x04       /* use include gene_version and transcript_version with
+                                            * ids if available */
 };
 
 enum genePredFields
 /* Bit set to indicate which optional fields are used.
  * N.B. value order must match order in genePred */
 {
     genePredNoOptFld      = 0x00,  /* use for no opt fields */
     genePredScoreFld      = 0x01,  /* score field */
     genePredName2Fld      = 0x02,  /* name2 field */
     genePredCdsStatFld    = 0x04,  /* cdsStart/EndStat fields */
     genePredExonFramesFld = 0x08,  /* exonFrames field */
     genePredAllFlds       = 0xFF   /* include all extended fields */
 };
 
 struct genePred