diff SNV/SNVMix2_source/SNVMix2-v0.12.1-rc1/samtools-0.1.6/kstring.h @ 0:74f5ea818cea

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SNV/SNVMix2_source/SNVMix2-v0.12.1-rc1/samtools-0.1.6/kstring.h	Wed Oct 12 19:50:38 2011 -0400
@@ -0,0 +1,68 @@
+#ifndef KSTRING_H
+#define KSTRING_H
+
+#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))
+#endif
+
+#ifndef KSTRING_T
+#define KSTRING_T kstring_t
+typedef struct __kstring_t {
+	size_t l, m;
+	char *s;
+} kstring_t;
+#endif
+
+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) {
+		s->m = s->l + l + 2;
+		kroundup32(s->m);
+		s->s = (char*)realloc(s->s, s->m);
+	}
+	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) {
+		s->m = s->l + 2;
+		kroundup32(s->m);
+		s->s = (char*)realloc(s->s, s->m);
+	}
+	s->s[s->l++] = c;
+	s->s[s->l] = 0;
+	return c;
+}
+
+static inline int *ksplit(kstring_t *s, int delimiter, int *n)
+{
+	int max = 0, *offsets = 0;
+	*n = ksplit_core(s->s, delimiter, &max, &offsets);
+	return offsets;
+}
+
+#endif