Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Adds checks for failed reads and gzip files with corrupt crc. #79

Merged
merged 1 commit into from
Feb 11, 2017
Merged

Adds checks for failed reads and gzip files with corrupt crc. #79

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
21 changes: 14 additions & 7 deletions kseq.h
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -44,6 +44,7 @@
type_t f; \
} kstream_t;

#define ks_err(ks) ((ks)->end == -1)
#define ks_eof(ks) ((ks)->is_eof && (ks)->begin >= (ks)->end)
#define ks_rewind(ks) ((ks)->is_eof = (ks)->begin = (ks)->end = 0)

Expand All @@ -66,11 +67,13 @@
#define __KS_GETC(__read, __bufsize) \
static inline int ks_getc(kstream_t *ks) \
{ \
if (ks_err(ks)) return -3; \
if (ks->is_eof && ks->begin >= ks->end) return -1; \
if (ks->begin >= ks->end) { \
ks->begin = 0; \
ks->end = __read(ks->f, ks->buf, __bufsize); \
if (ks->end == 0) { ks->is_eof = 1; return -1;} \
if (ks->end == -1) { ks->is_eof = 1; return -3;}\
} \
return (int)ks->buf[ks->begin++]; \
}
Expand All @@ -95,11 +98,13 @@ typedef struct __kstring_t {
str->l = append? str->l : 0; \
for (;;) { \
int i; \
if (ks_err(ks)) return -3; \
if (ks->begin >= ks->end) { \
if (!ks->is_eof) { \
ks->begin = 0; \
ks->end = __read(ks->f, ks->buf, __bufsize); \
if (ks->end == 0) { ks->is_eof = 1; break; } \
if (ks->end == -1) { ks->is_eof = 1; return -3; } \
} else break; \
} \
if (delimiter == KS_SEP_LINE) { \
Expand Down Expand Up @@ -167,25 +172,26 @@ typedef struct __kstring_t {
>=0 length of the sequence (normal)
-1 end-of-file
-2 truncated quality string
-3 error reading stream
*/
#define __KSEQ_READ(SCOPE) \
SCOPE int kseq_read(kseq_t *seq) \
{ \
int c; \
int c,r; \
kstream_t *ks = seq->f; \
if (seq->last_char == 0) { /* then jump to the next header line */ \
while ((c = ks_getc(ks)) != -1 && c != '>' && c != '@'); \
if (c == -1) return -1; /* end of file */ \
while ((c = ks_getc(ks)) >= 0 && c != '>' && c != '@'); \
if (c < 0) return c; /* end of file or error*/ \
seq->last_char = c; \
} /* else: the first header char has been read in the previous call */ \
seq->comment.l = seq->seq.l = seq->qual.l = 0; /* reset all members */ \
if (ks_getuntil(ks, 0, &seq->name, &c) < 0) return -1; /* normal exit: EOF */ \
if ((r=ks_getuntil(ks, 0, &seq->name, &c)) < 0) return r; /* normal exit: EOF or error */ \
if (c != '\n') ks_getuntil(ks, KS_SEP_LINE, &seq->comment, 0); /* read FASTA/Q comment */ \
if (seq->seq.s == 0) { /* we can do this in the loop below, but that is slower */ \
seq->seq.m = 256; \
seq->seq.s = (char*)malloc(seq->seq.m); \
} \
while ((c = ks_getc(ks)) != -1 && c != '>' && c != '+' && c != '@') { \
while ((c = ks_getc(ks)) >= 0 && c != '>' && c != '+' && c != '@') { \
if (c == '\n') continue; /* skip empty lines */ \
seq->seq.s[seq->seq.l++] = c; /* this is safe: we always have enough space for 1 char */ \
ks_getuntil2(ks, KS_SEP_LINE, &seq->seq, 0, 1); /* read the rest of the line */ \
Expand All @@ -202,9 +208,10 @@ typedef struct __kstring_t {
seq->qual.m = seq->seq.m; \
seq->qual.s = (char*)realloc(seq->qual.s, seq->qual.m); \
} \
while ((c = ks_getc(ks)) != -1 && c != '\n'); /* skip the rest of '+' line */ \
while ((c = ks_getc(ks)) >= 0 && c != '\n'); /* skip the rest of '+' line */ \
if (c == -1) return -2; /* error: no quality string */ \
while (ks_getuntil2(ks, KS_SEP_LINE, &seq->qual, 0, 1) >= 0 && seq->qual.l < seq->seq.l); \
while ((c = ks_getuntil2(ks, KS_SEP_LINE, &seq->qual, 0, 1) >= 0 && seq->qual.l < seq->seq.l)); \
if (c == -3) return -3; /* stream error */ \
seq->last_char = 0; /* we have not come to the next header line */ \
if (seq->seq.l != seq->qual.l) return -2; /* error: qual string is of a different length */ \
return seq->seq.l; \
Expand Down