--- /dev/null
+#include "pysam.h"
+
+#include <stdarg.h>
+#include <stdio.h>
+#include <ctype.h>
+#include <string.h>
+#include <stdint.h>
+#include "kstring.h"
+
+int ksprintf(kstring_t *s, const char *fmt, ...)
+{
+ va_list ap;
+ int l;
+ va_start(ap, fmt);
+ l = vsnprintf(s->s + s->l, s->m - s->l, fmt, ap); // This line does not work with glibc 2.0. See `man snprintf'.
+ va_end(ap);
+ if (l + 1 > s->m - s->l) {
+ s->m = s->l + l + 2;
+ kroundup32(s->m);
+ s->s = (char*)realloc(s->s, s->m);
+ va_start(ap, fmt);
+ l = vsnprintf(s->s + s->l, s->m - s->l, fmt, ap);
+ }
+ va_end(ap);
+ s->l += l;
+ return l;
+}
+
+char *kstrtok(const char *str, const char *sep, ks_tokaux_t *aux)
+{
+ const char *p, *start;
+ if (sep) { // set up the table
+ if (str == 0 && (aux->tab[0]&1)) return 0; // no need to set up if we have finished
+ aux->finished = 0;
+ if (sep[1]) {
+ aux->sep = -1;
+ aux->tab[0] = aux->tab[1] = aux->tab[2] = aux->tab[3] = 0;
+ for (p = sep; *p; ++p) aux->tab[*p>>6] |= 1ull<<(*p&0x3f);
+ } else aux->sep = sep[0];
+ }
+ if (aux->finished) return 0;
+ else if (str) aux->p = str - 1, aux->finished = 0;
+ if (aux->sep < 0) {
+ for (p = start = aux->p + 1; *p; ++p)
+ if (aux->tab[*p>>6]>>(*p&0x3f)&1) break;
+ } else {
+ for (p = start = aux->p + 1; *p; ++p)
+ if (*p == aux->sep) break;
+ }
+ aux->p = p; // end of token
+ if (*p == 0) aux->finished = 1; // no more tokens
+ return (char*)start;
+}
+
+// s MUST BE a null terminated string; l = strlen(s)
+int ksplit_core(char *s, int delimiter, int *_max, int **_offsets)
+{
+ int i, n, max, last_char, last_start, *offsets, l;
+ n = 0; max = *_max; offsets = *_offsets;
+ l = strlen(s);
+
+#define __ksplit_aux do { \
+ if (_offsets) { \
+ s[i] = 0; \
+ if (n == max) { \
+ max = max? max<<1 : 2; \
+ offsets = (int*)realloc(offsets, sizeof(int) * max); \
+ } \
+ offsets[n++] = last_start; \
+ } else ++n; \
+ } while (0)
+
+ for (i = 0, last_char = last_start = 0; i <= l; ++i) {
+ if (delimiter == 0) {
+ if (isspace(s[i]) || s[i] == 0) {
+ if (isgraph(last_char)) __ksplit_aux; // the end of a field
+ } else {
+ if (isspace(last_char) || last_char == 0) last_start = i;
+ }
+ } else {
+ if (s[i] == delimiter || s[i] == 0) {
+ if (last_char != 0 && last_char != delimiter) __ksplit_aux; // the end of a field
+ } else {
+ if (last_char == delimiter || last_char == 0) last_start = i;
+ }
+ }
+ last_char = s[i];
+ }
+ *_max = max; *_offsets = offsets;
+ return n;
+}
+
+/**********************
+ * Boyer-Moore search *
+ **********************/
+
+typedef unsigned char ubyte_t;
+
+// reference: http://www-igm.univ-mlv.fr/~lecroq/string/node14.html
+static int *ksBM_prep(const ubyte_t *pat, int m)
+{
+ int i, *suff, *prep, *bmGs, *bmBc;
+ prep = calloc(m + 256, sizeof(int));
+ bmGs = prep; bmBc = prep + m;
+ { // preBmBc()
+ for (i = 0; i < 256; ++i) bmBc[i] = m;
+ for (i = 0; i < m - 1; ++i) bmBc[pat[i]] = m - i - 1;
+ }
+ suff = calloc(m, sizeof(int));
+ { // suffixes()
+ int f = 0, g;
+ suff[m - 1] = m;
+ g = m - 1;
+ for (i = m - 2; i >= 0; --i) {
+ if (i > g && suff[i + m - 1 - f] < i - g)
+ suff[i] = suff[i + m - 1 - f];
+ else {
+ if (i < g) g = i;
+ f = i;
+ while (g >= 0 && pat[g] == pat[g + m - 1 - f]) --g;
+ suff[i] = f - g;
+ }
+ }
+ }
+ { // preBmGs()
+ int j = 0;
+ for (i = 0; i < m; ++i) bmGs[i] = m;
+ for (i = m - 1; i >= 0; --i)
+ if (suff[i] == i + 1)
+ for (; j < m - 1 - i; ++j)
+ if (bmGs[j] == m)
+ bmGs[j] = m - 1 - i;
+ for (i = 0; i <= m - 2; ++i)
+ bmGs[m - 1 - suff[i]] = m - 1 - i;
+ }
+ free(suff);
+ return prep;
+}
+
+void *kmemmem(const void *_str, int n, const void *_pat, int m, int **_prep)
+{
+ int i, j, *prep = 0, *bmGs, *bmBc;
+ const ubyte_t *str, *pat;
+ str = (const ubyte_t*)_str; pat = (const ubyte_t*)_pat;
+ prep = (_prep == 0 || *_prep == 0)? ksBM_prep(pat, m) : *_prep;
+ if (_prep && *_prep == 0) *_prep = prep;
+ bmGs = prep; bmBc = prep + m;
+ j = 0;
+ while (j <= n - m) {
+ for (i = m - 1; i >= 0 && pat[i] == str[i+j]; --i);
+ if (i >= 0) {
+ int max = bmBc[str[i+j]] - m + 1 + i;
+ if (max < bmGs[i]) max = bmGs[i];
+ j += max;
+ } else return (void*)(str + j);
+ }
+ if (_prep == 0) free(prep);
+ return 0;
+}
+
+char *kstrstr(const char *str, const char *pat, int **_prep)
+{
+ return (char*)kmemmem(str, strlen(str), pat, strlen(pat), _prep);
+}
+
+char *kstrnstr(const char *str, const char *pat, int n, int **_prep)
+{
+ return (char*)kmemmem(str, n, pat, strlen(pat), _prep);
+}
+
+/***********************
+ * The main() function *
+ ***********************/
+
+#ifdef KSTRING_MAIN
+#include <stdio.h>
+int main()
+{
+ kstring_t *s;
+ int *fields, n, i;
+ ks_tokaux_t aux;
+ char *p;
+ s = (kstring_t*)calloc(1, sizeof(kstring_t));
+ // test ksprintf()
+ ksprintf(s, " abcdefg: %d ", 100);
+ printf("'%s'\n", s->s);
+ // test ksplit()
+ fields = ksplit(s, 0, &n);
+ for (i = 0; i < n; ++i)
+ printf("field[%d] = '%s'\n", i, s->s + fields[i]);
+ // test kstrtok()
+ s->l = 0;
+ for (p = kstrtok("ab:cde:fg/hij::k", ":/", &aux); p; p = kstrtok(0, 0, &aux)) {
+ kputsn(p, aux.p - p, s);
+ kputc('\n', s);
+ }
+ printf("%s", s->s);
+ // free
+ free(s->s); free(s); free(fields);
+
+ {
+ static char *str = "abcdefgcdgcagtcakcdcd";
+ static char *pat = "cd";
+ char *ret, *s = str;
+ int *prep = 0;
+ while ((ret = kstrstr(s, pat, &prep)) != 0) {
+ printf("match: %s\n", ret);
+ s = ret + prep[0];
+ }
+ free(prep);
+ }
+ return 0;
+}
+#endif
projects / pysam.git / blobdiff