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Fix ks_getuntil2() extra empty record at EOF bug

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When the stream is an exact multiple of the buffer size, ks_getuntil2()
was returning a final empty record when it should have returned -1.
Fixed by moving the "EOF => return -1" check to after the read loop.

(See samtools/samtools#318 for an example of an error caused by a
spurious empty line at the end of a SAM file.)
This commit is contained in:
John Marshall 2014-11-13 14:28:46 +00:00
parent fa08681542
commit d60e5fc719
1 changed files with 3 additions and 1 deletions
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4
kseq.h
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@ -90,9 +90,9 @@ typedef struct __kstring_t {
#define __KS_GETUNTIL(__read, __bufsize) \
static int ks_getuntil2(kstream_t *ks, int delimiter, kstring_t *str, int *dret, int append) \
{ \
int gotany = 0; \
if (dret) *dret = 0; \
str->l = append? str->l : 0; \
if (ks->begin >= ks->end && ks->is_eof) return -1; \
for (;;) { \
int i; \
if (ks->begin >= ks->end) { \
@ -120,6 +120,7 @@ typedef struct __kstring_t {
kroundup32(str->m); \
str->s = (char*)realloc(str->s, str->m); \
} \
gotany = 1; \
memcpy(str->s + str->l, ks->buf + ks->begin, i - ks->begin); \
str->l = str->l + (i - ks->begin); \
ks->begin = i + 1; \
@ -128,6 +129,7 @@ typedef struct __kstring_t {
break; \
} \
} \
if (!gotany && ks_eof(ks)) return -1; \
if (str->s == 0) { \
str->m = 1; \
str->s = (char*)calloc(1, 1); \