ad3a176457ad1d21a0fedc47f349ec3484e751f1
angie
  Fri Feb 9 16:27:51 2018 -0800
Cleaning up some old ugliness about the size parameter to isAllDna and isAllNt.
hgc's printSnpAlignment code that parsed snpNNN.fa was using lineSize as length
but lineSize is length+1.  Then isAllDna was written with "i<size-1" as the
loop test instead of "i < size".  I didn't fix that properly when I separated
out isAllNt from isAllDna.
Later, I (re?)discovered that isAllNt needed length+1 as its size and just
added some FIXME comments.  Thanks Brian R for prodding me to actually fix it.
refs #20895

diff --git src/lib/dnautil.c src/lib/dnautil.c
index 6d81ba5..9ee6d78 100644
--- src/lib/dnautil.c
+++ src/lib/dnautil.c
@@ -1065,46 +1065,38 @@
 
 dnaUtilOpen();
 for (i=0; i<size; ++i)
     {
     if (ntChars[(int)poly[i]])
 	dnaCount += 1;
     }
 return (dnaCount >= round(0.9 * size));
 }
 
 boolean isAllNt(char *seq, int size)
 /* Return TRUE if all letters in seq are ACGTNU-. */
 {
 int i;
 dnaUtilOpen();
-for (i=0; i<size-1; ++i)
+for (i = 0;  i < size;  ++i)
     {
     if (ntChars[(int)seq[i]] == 0)
 	return FALSE;
     }
 return TRUE;
 }
 
-boolean isAllDna(char *poly, int size)
-/* Return TRUE if size is great than 1 and letters in poly are 100% ACGTNU- */
-{
-if (size <= 1)
-    return FALSE;
-return isAllNt(poly, size);
-}
-
 
 
 /* Tables to convert from 0-20 to ascii single letter representation
  * of proteins. */
 int aaVal[256];
 AA valToAa[21];
 
 AA aaChars[256];	/* 0 except for value aa characters.  Converts to upper case rest. */
 
 struct aminoAcidTable
 /* A little info about each amino acid. */
     {
     int ix;
     char letter;
     char abbreviation[3];