Implemented Boyer-Moore search in the kstring library.

[samtools.git] / kstring.h

diff --git a/kstring.h b/kstring.h
index 221ade2472655ba842477b1249feb7ca7209631c..99ab259462ea8c0fc3dc2c198705f9d3c3d8dac8 100644 (file)
--- a/kstring.h
+++ b/kstring.h
@@ -19,6 +19,14 @@ typedef struct __kstring_t {
 int ksprintf(kstring_t *s, const char *fmt, ...);
 int ksplit_core(char *s, int delimiter, int *_max, int **_offsets);
 
+// 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)
 {
        if (s->l + l + 1 >= s->m) {