a1c329068ad18aa4093972b501e6324f8bcdb398
angie
  Fri Sep 16 17:19:30 2016 -0700
Parse HGVS position ranges and coding terms' UTR and intron coordinates.
When the chromAlias table is present, this also now supports NC_*:g. terms.
The sequence change part is no longer parsed -- it's not necessary for mapping
to genomic ranges, although it will be necessary in order for hgVai to take
HGVS input.
This does not yet support ranges-of-ranges but neither does Mutalyzer.  This
also doesn't support uncertain positions ('?').  Like complex sequence changes,
those can wait until we have a sophisticated parser.
We also support some new not-quite-HGVS forms: geneSymbol and protein pos only,
or geneSymbol and c.<valid position range>.
refs #15071

diff --git src/lib/dnautil.c src/lib/dnautil.c
index 6c14a58..8687e91 100644
--- src/lib/dnautil.c
+++ src/lib/dnautil.c
@@ -1171,46 +1171,30 @@
 /* Initialize stuff herein. */
 {
 static boolean opened = FALSE;
 if (!opened)
     {
     checkSizeTypes();
     initNtVal();
     initAaVal();
     initNtChars();
     initNtMixedCaseChars();
     initNtCompTable();
     opened = TRUE;
     }
 }
 
-boolean aaToArbitraryCodon(char aa, char *dest)
-/* Reverse-translate aa back into one of its codons, return TRUE if successful.
- * Writes 3 characters at the start of dest; does not null-terminate the codon string. */
-{
-int ix;
-for (ix = 0;  ix < ArraySize(codonTable);  ix++)
-    {
-    if (toupper(aa) == codonTable[ix].protCode)
-        {
-        strncpy(dest, codonTable[ix].codon, 3);
-        return TRUE;
-        }
-    }
-return FALSE;
-}
-
 char aaAbbrToLetter(char *abbr)
 /* Convert an AA abbreviation such as "Ala", "Asp" etc., to its single letter code
  * such as "A", "D" etc.  Return the null char '\0' if abbr is not found. */
 {
 // Lowercase for comparison.
 char abbrLC[4];
 safencpy(abbrLC, sizeof(abbrLC), abbr, 3);
 toLowerN(abbrLC, 3);
 int ix;
 for (ix = 0;  ix < ArraySize(aminoAcidTable);  ix++)
     {
     if (sameStringN(abbrLC, aminoAcidTable[ix].abbreviation, 3))
         return aminoAcidTable[ix].letter;
     }
 return '\0';