Complain when BAM cannot be open. Severe bug fixed in -m haploid calling.

[samtools.git] / kstring.c

diff --git a/kstring.c b/kstring.c
index a09180bde9fe38fe7f7fe255de1708f22c3945b7..b8ff45c758128c6760c494b8c97d7e06d2a676bd 100644 (file)
--- a/kstring.c
+++ b/kstring.c
@@ -29,16 +29,24 @@ char *kstrtok(const char *str, const char *sep, ks_tokaux_t *aux)
        const char *p, *start;
        if (sep) { // set up the table
                if (str == 0 && (aux->tab[0]&1)) return 0; // no need to set up if we have finished
-               aux->tab[0] = aux->tab[1] = aux->tab[2] = aux->tab[3] = 0;
-               for (p = sep; *p; ++p)
-                       aux->tab[*p/64] |= 1ull<<(*p%64);
+               aux->finished = 0;
+               if (sep[1]) {
+                       aux->sep = -1;
+                       aux->tab[0] = aux->tab[1] = aux->tab[2] = aux->tab[3] = 0;
+                       for (p = sep; *p; ++p) aux->tab[*p>>6] |= 1ull<<(*p&0x3f);
+               } else aux->sep = sep[0];
+       }
+       if (aux->finished) return 0;
+       else if (str) aux->p = str - 1, aux->finished = 0;
+       if (aux->sep < 0) {
+               for (p = start = aux->p + 1; *p; ++p)
+                       if (aux->tab[*p>>6]>>(*p&0x3f)&1) break;
+       } else {
+               for (p = start = aux->p + 1; *p; ++p)
+                       if (*p == aux->sep) break;
        }
-       if (str) aux->p = str - 1, aux->tab[0] &= ~1ull;
-       else if (aux->tab[0]&1) return 0;
-       for (p = start = aux->p + 1; *p; ++p)
-               if (aux->tab[*p/64]>>(*p%64)) break;
        aux->p = p; // end of token
-       if (*p == 0) aux->tab[0] |= 1; // no more tokens
+       if (*p == 0) aux->finished = 1; // no more tokens
        return (char*)start;
 }
 
@@ -90,13 +98,13 @@ typedef unsigned char ubyte_t;
 static int *ksBM_prep(const ubyte_t *pat, int m)
 {
        int i, *suff, *prep, *bmGs, *bmBc;
-       prep = calloc(m + 256, sizeof(int));
+       prep = (int*)calloc(m + 256, sizeof(int));
        bmGs = prep; bmBc = prep + m;
        { // preBmBc()
                for (i = 0; i < 256; ++i) bmBc[i] = m;
                for (i = 0; i < m - 1; ++i) bmBc[pat[i]] = m - i - 1;
        }
-       suff = calloc(m, sizeof(int));
+       suff = (int*)calloc(m, sizeof(int));
        { // suffixes()
                int f = 0, g;
                suff[m - 1] = m;