In version 1.8, there are no binary files to remove from the upstream tarball.
[samtools.git] / kstring.c
1 #include <stdarg.h>
2 #include <stdio.h>
3 #include <ctype.h>
4 #include <string.h>
5 #include <stdint.h>
6 #include "kstring.h"
7
8 int ksprintf(kstring_t *s, const char *fmt, ...)
9 {
10         va_list ap;
11         int l;
12         va_start(ap, fmt);
13         l = vsnprintf(s->s + s->l, s->m - s->l, fmt, ap); // This line does not work with glibc 2.0. See `man snprintf'.
14         va_end(ap);
15         if (l + 1 > s->m - s->l) {
16                 s->m = s->l + l + 2;
17                 kroundup32(s->m);
18                 s->s = (char*)realloc(s->s, s->m);
19                 va_start(ap, fmt);
20                 l = vsnprintf(s->s + s->l, s->m - s->l, fmt, ap);
21         }
22         va_end(ap);
23         s->l += l;
24         return l;
25 }
26
27 // s MUST BE a null terminated string; l = strlen(s)
28 int ksplit_core(char *s, int delimiter, int *_max, int **_offsets)
29 {
30         int i, n, max, last_char, last_start, *offsets, l;
31         n = 0; max = *_max; offsets = *_offsets;
32         l = strlen(s);
33         
34 #define __ksplit_aux do {                                                                                               \
35                 if (_offsets) {                                                                                                 \
36                         s[i] = 0;                                                                                                       \
37                         if (n == max) {                                                                                         \
38                                 max = max? max<<1 : 2;                                                                  \
39                                 offsets = (int*)realloc(offsets, sizeof(int) * max);    \
40                         }                                                                                                                       \
41                         offsets[n++] = last_start;                                                                      \
42                 } else ++n;                                                                                                             \
43         } while (0)
44
45         for (i = 0, last_char = last_start = 0; i <= l; ++i) {
46                 if (delimiter == 0) {
47                         if (isspace(s[i]) || s[i] == 0) {
48                                 if (isgraph(last_char)) __ksplit_aux; // the end of a field
49                         } else {
50                                 if (isspace(last_char) || last_char == 0) last_start = i;
51                         }
52                 } else {
53                         if (s[i] == delimiter || s[i] == 0) {
54                                 if (last_char != 0 && last_char != delimiter) __ksplit_aux; // the end of a field
55                         } else {
56                                 if (last_char == delimiter || last_char == 0) last_start = i;
57                         }
58                 }
59                 last_char = s[i];
60         }
61         *_max = max; *_offsets = offsets;
62         return n;
63 }
64
65 /**********************
66  * Boyer-Moore search *
67  **********************/
68
69 // reference: http://www-igm.univ-mlv.fr/~lecroq/string/node14.html
70 int *ksBM_prep(const uint8_t *pat, int m)
71 {
72         int i, *suff, *prep, *bmGs, *bmBc;
73         prep = calloc(m + 256, 1);
74         bmGs = prep; bmBc = prep + m;
75         { // preBmBc()
76                 for (i = 0; i < 256; ++i) bmBc[i] = m;
77                 for (i = 0; i < m - 1; ++i) bmBc[pat[i]] = m - i - 1;
78         }
79         suff = calloc(m, sizeof(int));
80         { // suffixes()
81                 int f = 0, g;
82                 suff[m - 1] = m;
83                 g = m - 1;
84                 for (i = m - 2; i >= 0; --i) {
85                         if (i > g && suff[i + m - 1 - f] < i - g)
86                                 suff[i] = suff[i + m - 1 - f];
87                         else {
88                                 if (i < g) g = i;
89                                 f = i;
90                                 while (g >= 0 && pat[g] == pat[g + m - 1 - f]) --g;
91                                 suff[i] = f - g;
92                         }
93                 }
94         }
95         { // preBmGs()
96                 int j = 0;
97                 for (i = 0; i < m; ++i) bmGs[i] = m;
98                 for (i = m - 1; i >= 0; --i)
99                         if (suff[i] == i + 1)
100                                 for (; j < m - 1 - i; ++j)
101                                         if (bmGs[j] == m)
102                                                 bmGs[j] = m - 1 - i;
103                 for (i = 0; i <= m - 2; ++i)
104                         bmGs[m - 1 - suff[i]] = m - 1 - i;
105         }
106         free(suff);
107         return prep;
108 }
109
110 int *ksBM_search(const uint8_t *str, int n, const uint8_t *pat, int m, int *_prep, int *n_matches)
111 {
112         int i, j, *prep, *bmGs, *bmBc;
113         int *matches = 0, mm = 0, nm = 0;
114         prep = _prep? _prep : ksBM_prep(pat, m);
115         bmGs = prep; bmBc = prep + m;
116         j = 0;
117         while (j <= n - m) {
118                 for (i = m - 1; i >= 0 && pat[i] == str[i+j]; --i);
119                 if (i < 0) {
120                         if (nm == mm) {
121                                 mm = mm? mm<<1 : 1;
122                                 matches = realloc(matches, mm * sizeof(int));
123                         }
124                         matches[nm++] = j;
125                         j += bmGs[0];
126                 } else {
127                         int max = bmBc[str[i+j]] - m + 1 + i;
128                         if (max < bmGs[i]) max = bmGs[i];
129                         j += max;
130                 }
131         }
132         *n_matches = nm;
133         if (_prep == 0) free(prep);
134         return matches;
135 }
136
137 #ifdef KSTRING_MAIN
138 #include <stdio.h>
139 int main()
140 {
141         kstring_t *s;
142         int *fields, n, i;
143         s = (kstring_t*)calloc(1, sizeof(kstring_t));
144         // test ksprintf()
145         ksprintf(s, " abcdefg:    %d ", 100);
146         printf("'%s'\n", s->s);
147         // test ksplit()
148         fields = ksplit(s, 0, &n);
149         for (i = 0; i < n; ++i)
150                 printf("field[%d] = '%s'\n", i, s->s + fields[i]);
151         free(s);
152
153         {
154                 static char *str = "abcdefgcdg";
155                 static char *pat = "cd";
156                 int n, *matches;
157                 matches = ksBM_search(str, strlen(str), pat, strlen(pat), 0, &n);
158                 printf("%d: \n", n);
159                 for (i = 0; i < n; ++i)
160                         printf("- %d\n", matches[i]);
161                 free(matches);
162         }
163         return 0;
164 }
165 #endif