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/inc/dnautil.h src/inc/dnautil.h
index dc1417a..2730569 100644
--- src/inc/dnautil.h
+++ src/inc/dnautil.h
@@ -255,24 +255,20 @@
  * trimmed too.  Returns number of bases trimmed.  */
 
 int maskHeadPolyT(DNA *dna, int size);
 /* Convert PolyT at start.  This allows a few non-T's as noise to be 
  * trimmed too.  Returns number of bases trimmed.  */
 
 boolean isDna(char *poly, int size);
 /* Return TRUE if letters in poly are at least 90% ACGTNU- */
 
 boolean isAllDna(char *poly, int size);
 /* Return TRUE if size is great than 1 and all letters in poly are 100% ACGTNU- */
 
 boolean isAllNt(char *seq, int size);
 /* Return TRUE if all letters in seq are ACGTNU-. */
 
-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. */
-
 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. */
 
 #endif /* DNAUTIL_H */