be072873575820f30b4da2eedd2d99c95a25c21c
cline
  Tue Feb 15 15:30:20 2011 -0800
When recording a selenocysteine exception, save the specific information on the exception in the hash.  This will be useful later in txCdsPick.c
diff --git src/hg/lib/genbank.c src/hg/lib/genbank.c
index a831c8e..ba529ac 100644
--- src/hg/lib/genbank.c
+++ src/hg/lib/genbank.c
@@ -193,31 +193,31 @@
 /* Will read a genbank exceptions file, and return two hashes parsed out of
  * it filled with the accessions having the two exceptions we can handle, 
  * selenocysteines, and alternative start codons. */
 {
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 struct hash *scHash = *retSelenocysteineHash  = hashNew(0);
 struct hash *altStartHash = *retAltStartHash = hashNew(0);
 char *row[3];
 while (lineFileRowTab(lf, row))
     {
     struct lineFile *lf = lineFileOpen(fileName, TRUE);
     char *row[3];
     while (lineFileRow(lf, row))
         {
 	if (sameString(row[1], "translExcept") && (stringIn("aa:Sec", row[2]) != NULL))
-	    hashAdd(scHash, row[0], NULL);
+	    hashAdd(scHash, row[0], row[2]);
 	if (sameString(row[1], "exception") 
 		&& sameString(row[2], "alternative_start_codon"))
 	    hashAdd(altStartHash, row[0], NULL);
 	}
     }
 lineFileClose(&lf);
 }
 
 struct genbankCds genbankCdsToGenome(struct genbankCds* cds, struct psl *psl)
 /* Convert set cdsStart/end from mrna to genomic coordinates using an
  * alignment.  Returns a genbankCds object with genomic (positive strand)
  * coordinates */
 {
 // FIXME: this is used only by genePred code, but since  frame was added,
 // genome mapping  of CDS is computed both here and genePred.getFrame().