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/iupac.c src/lib/iupac.c
index 9289d51..1fe9d44 100644
--- src/lib/iupac.c
+++ src/lib/iupac.c
@@ -94,49 +94,36 @@
 {
 char c;
 while ((c = *in++) != 0)
     {
     c = tolower(c);
     if (isIupacLower(c))
        *out++ = c;
     }
 *out++ = 0;
 }
 
 boolean anyIupac(char *s)
 /* Return TRUE if there are any IUPAC ambiguity codes in s */
 {
 dnaUtilOpen();
-int c;
+char c;
 while ((c = *s++) != 0)
     {
-    switch (c)
-	{
-	case 'r':
-	case 'y':
-	case 's':
-	case 'w':
-	case 'k':
-	case 'm':
-	case 'b':
-	case 'd':
-	case 'h':
-	case 'v':
-	case 'n':
+    if (isIupacAmbiguous(c))
         return TRUE;
     }
-    }
 return FALSE;
 }
 
 char iupacComplementBaseLower(char iupac)
 /* Return IUPAC complement for a single base */
 {
 switch (iupac)
     {
     case 'a':
         return 't';
     case 'c':
         return 'g';
     case 'g':
         return 'c';
     case 't':