Patched the example makefile to not use samtools pileup, deprecated.

[samtools.git] / kstring.h

diff --git a/kstring.h b/kstring.h
index f4e5a99df5b03364166338e55799edbc41b1cae4..ec5775b485316c4faaa190a2c501a57fc188985c 100644 (file)
--- a/kstring.h
+++ b/kstring.h
@@ -17,17 +17,32 @@ typedef struct __kstring_t {
 } kstring_t;
 #endif
 
-int ksprintf(kstring_t *s, const char *fmt, ...);
-int ksplit_core(char *s, int delimiter, int *_max, int **_offsets);
+typedef struct {
+       uint64_t tab[4];
+       int sep, finished;
+       const char *p; // end of the current token
+} ks_tokaux_t;
 
-// calculate the auxiliary array, allocated by calloc()
-int *ksBM_prep(const uint8_t *pat, int m);
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+       int ksprintf(kstring_t *s, const char *fmt, ...);
+       int ksplit_core(char *s, int delimiter, int *_max, int **_offsets);
+       char *kstrstr(const char *str, const char *pat, int **_prep);
+       char *kstrnstr(const char *str, const char *pat, int n, int **_prep);
+       void *kmemmem(const void *_str, int n, const void *_pat, int m, int **_prep);
 
-/* Search pat in str and returned the list of matches. The size of the
- * list is returned as n_matches. _prep is the array returned by
- * ksBM_prep(). If it is a NULL pointer, ksBM_prep() will be called. */
-int *ksBM_search(const uint8_t *str, int n, const uint8_t *pat, int m, int *_prep, int *n_matches);
+       /* kstrtok() is similar to strtok_r() except that str is not
+        * modified and both str and sep can be NULL. For efficiency, it is
+        * actually recommended to set both to NULL in the subsequent calls
+        * if sep is not changed. */
+       char *kstrtok(const char *str, const char *sep, ks_tokaux_t *aux);
 
+#ifdef __cplusplus
+}
+#endif
+       
 static inline int kputsn(const char *p, int l, kstring_t *s)
 {
        if (s->l + l + 1 >= s->m) {
@@ -35,7 +50,7 @@ static inline int kputsn(const char *p, int l, kstring_t *s)
                kroundup32(s->m);
                s->s = (char*)realloc(s->s, s->m);
        }
-       strncpy(s->s + s->l, p, l);
+       memcpy(s->s + s->l, p, l);
        s->l += l;
        s->s[s->l] = 0;
        return l;
@@ -58,6 +73,40 @@ static inline int kputc(int c, kstring_t *s)
        return c;
 }
 
+static inline int kputw(int c, kstring_t *s)
+{
+       char buf[16];
+       int l, x;
+       if (c == 0) return kputc('0', s);
+       for (l = 0, x = c < 0? -c : c; x > 0; x /= 10) buf[l++] = x%10 + '0';
+       if (c < 0) buf[l++] = '-';
+       if (s->l + l + 1 >= s->m) {
+               s->m = s->l + l + 2;
+               kroundup32(s->m);
+               s->s = (char*)realloc(s->s, s->m);
+       }
+       for (x = l - 1; x >= 0; --x) s->s[s->l++] = buf[x];
+       s->s[s->l] = 0;
+       return 0;
+}
+
+static inline int kputuw(unsigned c, kstring_t *s)
+{
+       char buf[16];
+       int l, i;
+       unsigned x;
+       if (c == 0) return kputc('0', s);
+       for (l = 0, x = c; x > 0; x /= 10) buf[l++] = x%10 + '0';
+       if (s->l + l + 1 >= s->m) {
+               s->m = s->l + l + 2;
+               kroundup32(s->m);
+               s->s = (char*)realloc(s->s, s->m);
+       }
+       for (i = l - 1; i >= 0; --i) s->s[s->l++] = buf[i];
+       s->s[s->l] = 0;
+       return 0;
+}
+
 static inline int *ksplit(kstring_t *s, int delimiter, int *n)
 {
        int max = 0, *offsets = 0;