return 0;
}
-#define char2int(s) (((int)s[0])<<8|s[1])
-
int bcf_sync(int n_smpl, bcf1_t *b)
{
- char *p, *tmp[5], *s;
+ char *p, *tmp[5];
int i, n;
+ ks_tokaux_t aux;
// set ref, alt, flt, info, fmt
b->ref = b->alt = b->flt = b->info = b->fmt = 0;
for (p = b->str, n = 0; p < b->str + b->l_str; ++p)
memset(b->gi + old_m, 0, (b->m_gi - old_m) * sizeof(bcf_ginfo_t));
}
b->n_gi = n;
- for (p = s = b->fmt, n = 0; *p; ++p) {
- if (*p == ':' || *(p+1) == 0) {
- char *q = *p == ':'? p : p + 1;
- if ((q - s) != 2) return -2;
- b->gi[n].fmt = char2int(s);
- s = q;
- }
- }
+ for (p = kstrtok(b->fmt, ":", &aux), n = 0; p; p = kstrtok(0, 0, &aux))
+ b->gi[n++].fmt = bcf_str2int(p, aux.p - p);
// set gi[i].len
for (i = 0; i < b->n_gi; ++i) {
- if (b->gi[i].fmt == char2int("PL")) {
+ if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
b->gi[i].len = b->n_alleles * (b->n_alleles + 1) / 2;
- } else if (b->gi[i].fmt == char2int("DP") || b->gi[i].fmt == char2int("HQ")) {
+ } else if (b->gi[i].fmt == bcf_str2int("DP", 2) || b->gi[i].fmt == bcf_str2int("HQ", 2)) {
b->gi[i].len = 2;
- } else if (b->gi[i].fmt == char2int("GQ") || b->gi[i].fmt == char2int("GT")) {
+ } else if (b->gi[i].fmt == bcf_str2int("GQ", 2) || b->gi[i].fmt == bcf_str2int("GT", 2)) {
b->gi[i].len = 1;
- } else if (b->gi[i].fmt == char2int("GL")) {
+ } else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
b->gi[i].len = 4;
}
b->gi[i].data = realloc(b->gi[i].data, n_smpl * b->gi[i].len);
kputc('\t', &s);
for (i = 0; i < b->n_gi; ++i) {
if (i) kputc(':', &s);
- if (b->gi[i].fmt == char2int("PL")) {
+ if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
uint8_t *d = (uint8_t*)b->gi[i].data + j * x;
int k;
for (k = 0; k < x; ++k) {
if (k > 0) kputc(',', &s);
kputw(d[k], &s);
}
- } else if (b->gi[i].fmt == char2int("DP")) {
+ } else if (b->gi[i].fmt == bcf_str2int("DP", 2)) {
kputw(((uint16_t*)b->gi[i].data)[j], &s);
- } else if (b->gi[i].fmt == char2int("GQ")) {
+ } else if (b->gi[i].fmt == bcf_str2int("GQ", 2)) {
kputw(((uint8_t*)b->gi[i].data)[j], &s);
}
}
#include "bgzf.h"
typedef struct {
- int fmt, len; // len is the unit length
+ uint32_t fmt;
+ int len; // len is the unit length
void *data;
// derived info: fmt, len
} bcf_ginfo_t;
}
#endif
+static inline uint32_t bcf_str2int(const char *str, int l)
+{
+ int i;
+ uint32_t x = 0;
+ for (i = 0; i < l && i < 4; ++i) {
+ if (str[i] == 0) return x;
+ x = x<<8 | str[i];
+ }
+ return x;
+}
+
#endif
fprintf(stderr, "\n");
fprintf(stderr, "Usage: bcftools view [options] <in.bcf> [reg]\n\n");
fprintf(stderr, "Options: -c SNP calling\n");
+ fprintf(stderr, " -b output BCF instead of VCF\n");
fprintf(stderr, " -G suppress all individual genotype information\n");
fprintf(stderr, " -L discard the PL genotype field\n");
fprintf(stderr, " -v output potential variant sites only\n");
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->tab[0] = aux->tab[1] = aux->tab[2] = aux->tab[3] = 0;
+ for (p = sep; *p; ++p)
+ aux->tab[*p/64] |= 1ull<<(*p%64);
+ }
+ if (str) aux->p = str - 1, aux->tab[0] &= ~1ull;
+ else if (aux->tab[0]&1) return 0;
+ for (p = start = aux->p + 1; *p; ++p)
+ if (aux->tab[*p/64]>>(*p%64)) break;
+ aux->p = p; // end of token
+ if (*p == 0) aux->tab[0] |= 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)
{
* Boyer-Moore search *
**********************/
+typedef unsigned char ubyte_t;
+
// reference: http://www-igm.univ-mlv.fr/~lecroq/string/node14.html
-int *ksBM_prep(const uint8_t *pat, int m)
+static int *ksBM_prep(const ubyte_t *pat, int m)
{
int i, *suff, *prep, *bmGs, *bmBc;
- prep = calloc(m + 256, 1);
+ prep = calloc(m + 256, sizeof(int));
bmGs = prep; bmBc = prep + m;
{ // preBmBc()
for (i = 0; i < 256; ++i) bmBc[i] = m;
return prep;
}
-int *ksBM_search(const uint8_t *str, int n, const uint8_t *pat, int m, int *_prep, int *n_matches)
+void *kmemmem(const void *_str, int n, const void *_pat, int m, int **_prep)
{
- int i, j, *prep, *bmGs, *bmBc;
- int *matches = 0, mm = 0, nm = 0;
- prep = _prep? _prep : ksBM_prep(pat, m);
+ 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) {
- if (nm == mm) {
- mm = mm? mm<<1 : 1;
- matches = realloc(matches, mm * sizeof(int));
- }
- matches[nm++] = j;
- j += bmGs[0];
- } else {
+ 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);
}
- *n_matches = nm;
if (_prep == 0) free(prep);
- return matches;
+ 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);
fields = ksplit(s, 0, &n);
for (i = 0; i < n; ++i)
printf("field[%d] = '%s'\n", i, s->s + fields[i]);
- free(s);
+ // 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 = "abcdefgcdg";
+ static char *str = "abcdefgcdgcagtcakcdcd";
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);
+ 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;
}
} kstring_t;
#endif
-int ksprintf(kstring_t *s, const char *fmt, ...);
-int ksplit_core(char *s, int delimiter, int *_max, int **_offsets);
+typedef struct {
+ uint64_t tab[4];
+ const char *p; // end of the current token
+} ks_tokaux_t;
-// calculate the auxiliary array, allocated by calloc()
-int *ksBM_prep(const uint8_t *pat, int m);
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+ int ksprintf(kstring_t *s, const char *fmt, ...);
+ int ksplit_core(char *s, int delimiter, int *_max, int **_offsets);
+ char *kstrstr(const char *str, const char *pat, int **_prep);
+ char *kstrnstr(const char *str, const char *pat, int n, int **_prep);
+ void *kmemmem(const void *_str, int n, const void *_pat, int m, int **_prep);
-/* 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);
+ /* kstrtok() is similar to strtok_r() except that str is not
+ * modified and both str and sep can be NULL. For efficiency, it is
+ * actually recommended to set both to NULL in the subsequent calls
+ * if sep is not changed. */
+ char *kstrtok(const char *str, const char *sep, ks_tokaux_t *aux);
+#ifdef __cplusplus
+}
+#endif
+
static inline int kputsn(const char *p, int l, kstring_t *s)
{
if (s->l + l + 1 >= s->m) {
kroundup32(s->m);
s->s = (char*)realloc(s->s, s->m);
}
- strncpy(s->s + s->l, p, l);
+ memcpy(s->s + s->l, p, l);
s->l += l;
s->s[s->l] = 0;
return l;
projects / samtools.git / commitdiff