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#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;
}
// 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 *
**********************/
// reference: http://www-igm.univ-mlv.fr/~lecroq/string/node14.html
int *ksBM_prep(const uint8_t *pat, int m)
{
int i, *suff, *prep, *bmGs, *bmBc;
prep = calloc(m + 256, 1);
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;
}
int *ksBM_search(const uint8_t *str, int n, const uint8_t *pat, int m, int *_prep, int *n_matches)
{
int i, j, *prep, *bmGs, *bmBc;
int *matches = 0, mm = 0, nm = 0;
prep = _prep? _prep : ksBM_prep(pat, m);
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) {
if (nm == mm) {
mm = mm? mm<<1 : 1;
matches = realloc(matches, mm * sizeof(int));
}
matches[nm++] = j;
j += bmGs[0];
} else {
int max = bmBc[str[i+j]] - m + 1 + i;
if (max < bmGs[i]) max = bmGs[i];
j += max;
}
}
*n_matches = nm;
if (_prep == 0) free(prep);
return matches;
}
#ifdef KSTRING_MAIN
#include <stdio.h>
int main()
{
kstring_t *s;
int *fields, n, i;
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]);
free(s);
{
static char *str = "abcdefgcdg";
static char *pat = "cd";
int n, *matches;
matches = ksBM_search(str, strlen(str), pat, strlen(pat), 0, &n);
printf("%d: \n", n);
for (i = 0; i < n; ++i)
printf("- %d\n", matches[i]);
free(matches);
}
return 0;
}
#endif
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