A bug fix, "samtools view" is now working again.

[samtools.git] / kstring.h

diff --git a/kstring.h b/kstring.h
index 47d63f7690d7e146502856050b38a3699b810ba0..f4e5a99df5b03364166338e55799edbc41b1cae4 100644 (file)
--- a/kstring.h
+++ b/kstring.h
@@ -3,6 +3,7 @@
 
 #include <stdlib.h>
 #include <string.h>
+#include <stdint.h>
 
 #ifndef kroundup32
 #define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
@@ -19,19 +20,32 @@ typedef struct __kstring_t {
 int ksprintf(kstring_t *s, const char *fmt, ...);
 int ksplit_core(char *s, int delimiter, int *_max, int **_offsets);
 
-static inline int kputs(const char *p, kstring_t *s)
+// calculate the auxiliary array, allocated by calloc()
+int *ksBM_prep(const uint8_t *pat, int m);
+
+/* 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);
+
+static inline int kputsn(const char *p, int l, kstring_t *s)
 {
-       int l = strlen(p);
        if (s->l + l + 1 >= s->m) {
                s->m = s->l + l + 2;
                kroundup32(s->m);
                s->s = (char*)realloc(s->s, s->m);
        }
-       strcpy(s->s + s->l, p);
+       strncpy(s->s + s->l, p, l);
        s->l += l;
+       s->s[s->l] = 0;
        return l;
 }
 
+static inline int kputs(const char *p, kstring_t *s)
+{
+       return kputsn(p, strlen(p), s);
+}
+
 static inline int kputc(int c, kstring_t *s)
 {
        if (s->l + 1 >= s->m) {