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Merge pull request #19 from jkbonfield/master 

Error checking + updates from htslib
This commit is contained in:
Heng Li 2013-07-19 10:58:43 -07:00
parent af0848b627 133bb25dfe
commit cad4c57d97
2 changed files with 112 additions and 16 deletions
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25
kstring.c
View File

@ -67,15 +67,22 @@ int ksplit_core(char *s, int delimiter, int *_max, int **_offsets)
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; \
#define __ksplit_aux do { \
if (_offsets) { \
s[i] = 0; \
if (n == max) { \
int *tmp; \
max = max? max<<1 : 2; \
if ((tmp = (int*)realloc(offsets, sizeof(int) * max))) { \
offsets = tmp; \
} else { \
free(offsets); \
*_offsets = NULL; \
return 0; \
} \
} \
offsets[n++] = last_start; \
} else ++n; \
} while (0)
for (i = 0, last_char = last_start = 0; i <= l; ++i) {

103
kstring.h
View File

@ -30,6 +30,7 @@
#include <string.h>
#include <stdarg.h>
#include <stdint.h>
#include <stdio.h>
#ifndef kroundup32
#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
@ -77,21 +78,40 @@ extern "C" {
}
#endif
static inline void ks_resize(kstring_t *s, size_t size)
static inline int ks_resize(kstring_t *s, size_t size)
{
if (s->m < size) {
char *tmp;
s->m = size;
kroundup32(s->m);
s->s = (char*)realloc(s->s, s->m);
if ((tmp = (char*)realloc(s->s, s->m)))
s->s = tmp;
else
return -1;
}
return 0;
}
static inline char *ks_str(kstring_t *s)
{
return s->s;
}
static inline size_t ks_len(kstring_t *s)
{
return s->l;
}
static inline int kputsn(const char *p, int l, kstring_t *s)
{
if (s->l + l + 1 >= s->m) {
char *tmp;
s->m = s->l + l + 2;
kroundup32(s->m);
s->s = (char*)realloc(s->s, s->m);
if ((tmp = (char*)realloc(s->s, s->m)))
s->s = tmp;
else
return EOF;
}
memcpy(s->s + s->l, p, l);
s->l += l;
@ -107,26 +127,66 @@ static inline int kputs(const char *p, kstring_t *s)
static inline int kputc(int c, kstring_t *s)
{
if (s->l + 1 >= s->m) {
char *tmp;
s->m = s->l + 2;
kroundup32(s->m);
s->s = (char*)realloc(s->s, s->m);
if ((tmp = (char*)realloc(s->s, s->m)))
s->s = tmp;
else
return EOF;
}
s->s[s->l++] = c;
s->s[s->l] = 0;
return c;
}
static inline int kputc_(int c, kstring_t *s)
{
if (s->l + 1 > s->m) {
char *tmp;
s->m = s->l + 1;
kroundup32(s->m);
if ((tmp = (char*)realloc(s->s, s->m)))
s->s = tmp;
else
return EOF;
}
s->s[s->l++] = c;
return 1;
}
static inline int kputsn_(const void *p, int l, kstring_t *s)
{
if (s->l + l > s->m) {
char *tmp;
s->m = s->l + l;
kroundup32(s->m);
if ((tmp = (char*)realloc(s->s, s->m)))
s->s = tmp;
else
return EOF;
}
memcpy(s->s + s->l, p, l);
s->l += l;
return l;
}
static inline int kputw(int c, kstring_t *s)
{
char buf[16];
int l, x;
if (c == 0) return kputc('0', s);
for (l = 0, x = c < 0? -c : c; x > 0; x /= 10) buf[l++] = x%10 + '0';
if (c < 0) for (l = 0, x = c; x < 0; x /= 10) buf[l++] = '0' - (x%10);
else for (l = 0, x = c; x > 0; x /= 10) buf[l++] = x%10 + '0';
if (c < 0) buf[l++] = '-';
if (s->l + l + 1 >= s->m) {
char *tmp;
s->m = s->l + l + 2;
kroundup32(s->m);
s->s = (char*)realloc(s->s, s->m);
if ((tmp = (char*)realloc(s->s, s->m)))
s->s = tmp;
else
return EOF;
}
for (x = l - 1; x >= 0; --x) s->s[s->l++] = buf[x];
s->s[s->l] = 0;
@ -141,15 +201,44 @@ static inline int kputuw(unsigned c, kstring_t *s)
if (c == 0) return kputc('0', s);
for (l = 0, x = c; x > 0; x /= 10) buf[l++] = x%10 + '0';
if (s->l + l + 1 >= s->m) {
char *tmp;
s->m = s->l + l + 2;
kroundup32(s->m);
s->s = (char*)realloc(s->s, s->m);
if ((tmp = (char*)realloc(s->s, s->m)))
s->s = tmp;
else
return EOF;
}
for (i = l - 1; i >= 0; --i) s->s[s->l++] = buf[i];
s->s[s->l] = 0;
return 0;
}
static inline int kputl(long c, kstring_t *s)
{
char buf[32];
long l, x;
if (c == 0) return kputc('0', s);
for (l = 0, x = c < 0? -c : c; x > 0; x /= 10) buf[l++] = x%10 + '0';
if (c < 0) buf[l++] = '-';
if (s->l + l + 1 >= s->m) {
char *tmp;
s->m = s->l + l + 2;
kroundup32(s->m);
if ((tmp = (char*)realloc(s->s, s->m)))
s->s = tmp;
else
return EOF;
}
for (x = l - 1; x >= 0; --x) s->s[s->l++] = buf[x];
s->s[s->l] = 0;
return 0;
}
/*
* Returns 's' split by delimiter, with *n being the number of components;
* NULL on failue.
*/
static inline int *ksplit(kstring_t *s, int delimiter, int *n)
{
int max = 0, *offsets = 0;