Added notes on how the package is tested.

[samtools.git] / kstring.h

diff --git a/kstring.h b/kstring.h
index 221ade2472655ba842477b1249feb7ca7209631c..925117a38646ab4c1b82db01e46091f9e073eefd 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))
@@ -19,6 +20,14 @@ 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) {
@@ -49,6 +58,40 @@ 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;