bug fix in seg.sites + new option in base.freq

[ape.git] / src / dist_dna.c

diff --git a/src/dist_dna.c b/src/dist_dna.c
index d56c794334beee45f113cef278d5c38dea5a5147..2aa6da6be9531dd1c24ba7d5c90e66c9afe27cc1 100644 (file)
--- a/src/dist_dna.c
+++ b/src/dist_dna.c
@@ -1,4 +1,4 @@
-/* dist_dna.c       2008-12-22 */
+/* dist_dna.c       2009-09-16 */
 
 /* Copyright 2005-2008 Emmanuel Paradis
 
@@ -12,7 +12,7 @@
 #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
@@ -951,7 +951,7 @@ void distDNA_ParaLin_pairdel(unsigned char *x, int *n, int *s, double *d,
     }
 }
 
-void BaseProportion(unsigned char *x, int *n, double *BF)
+void BaseProportion(unsigned char *x, int *n, double *BF, int *freq)
 {
     int i, m;
 
@@ -967,7 +967,7 @@ void BaseProportion(unsigned char *x, int *n, double *BF)
            }
        }
     }
-    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)
@@ -981,7 +981,7 @@ 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;