-/* dist_dna.c 2008-12-22 */
+/* dist_dna.c 2009-09-16 */
/* Copyright 2005-2008 Emmanuel Paradis
#define LN4 1.386294361119890572454
/* returns 8 if the base is known surely, 0 otherwise */
-#define KnownBase(a) a & 8
+#define KnownBase(a) (a & 8)
/* returns 1 if the base is adenine surely, 0 otherwise */
#define IsAdenine(a) a == 136
}
}
-void BaseProportion(unsigned char *x, int *n, double *BF)
+void BaseProportion(unsigned char *x, int *n, double *BF, int *freq)
{
int i, m;
}
}
}
- for (i = 0; i < 4; i++) BF[i] /= m;
+ if (! *freq) for (i = 0; i < 4; i++) BF[i] /= m;
}
void SegSites(unsigned char *x, int *n, int *s, int *seg)
basis = x[i];
i++;
while (i < *n * (j + 1)) {
- if (x[i] == basis) i++;
+ if (!KnownBase(x[i]) || x[i] == basis) i++;
else {
seg[j] = 1;
break;