65479b434f3b7e556b78d1c75171fd3365e20272
angie
  Mon Oct 14 16:46:03 2013 -0700
isAllDna has a condition that surprised me (returns FALSE if size is 1),so I added isAllNt which has the behavior I expected.

diff --git src/inc/dnautil.h src/inc/dnautil.h
index 7ce450b..94b25af 100644
--- src/inc/dnautil.h
+++ src/inc/dnautil.h
@@ -240,21 +240,24 @@
 int headPolyTSizeLoose(DNA *dna, int size);
 /* Return size of PolyT at start (if present).  This allows a few non-T's as 
  * noise to be trimmed too, but skips last two tt for revcomp'd taa stop 
  * codon.  
  * It is less conservative in extending the polyA region than maskHeadPolyT. */
 
 int maskTailPolyA(DNA *dna, int size);
 /* Convert PolyA at end to n.  This allows a few non-A's as noise to be 
  * 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% ACGTU */
+/* Return TRUE if letters in poly are at least 90% ACGTNU- */
 
 boolean isAllDna(char *poly, int size);
-/* Return TRUE if letters in poly are 100% ACGTU */
+/* 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-. */
 
 #endif /* DNAUTIL_H */