37977956905d588f73ee5f635fae2f609cb40842
angie
  Wed Aug 9 12:52:00 2017 -0700
Assorted little util functions in support of adding HGVS output to hgVai -- refs #19968

diff --git src/inc/dnautil.h src/inc/dnautil.h
index 2730569..5f249fa 100644
--- src/inc/dnautil.h
+++ src/inc/dnautil.h
@@ -259,16 +259,23 @@
  * 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-. */
 
 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. */
 
+void aaToAbbr(char aa, char *abbrBuf, size_t abbrBufSize);
+/* Convert an AA single letter such as "A", "D" etc. to its abbreviation such as "Ala", "Asp" etc.
+ * abbrBufSize must be at least 4.  If aa is not found, "?%c?",aa is written into abbrBuf. */
+
+void trimRefAlt(char *ref, char *alt, uint *pStart, uint *pEnd, int *pRefLen, int *pAltLen);
+/* If ref and alt have identical bases at beginning and/or end, trim those & update all params. */
+
 #endif /* DNAUTIL_H */