aaf72102b545c05c42f66b7a3fc22d65b1ecf4fe
angie
  Mon Aug 8 14:12:39 2016 -0700
Added recognition of a small subset of HGVS terms: coding (c.) SNVs relative to RefSeq NM_ or LRG transcript IDs,
and protein (p.) simple substitutions relative to NP_.
Also accepted (not HGVS but similar and popular): geneSymbol and abbreviated protein subst like "ALK G1494E".
hgFind will map terms to the current genome if possible, and will display warnings about unrecognized accessions,
out-of-bounds coordinates and mismatching reference alleles.
refs #15071, #15554

diff --git src/inc/dnautil.h src/inc/dnautil.h
index 2a9b15f..dc1417a 100644
--- src/inc/dnautil.h
+++ src/inc/dnautil.h
@@ -255,16 +255,24 @@
  * 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 */