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Backport attractivechaos/klib#78 to htslib. #1582

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merged 1 commit into from
Mar 13, 2023
Merged

Backport attractivechaos/klib#78 to htslib. #1582

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26 changes: 16 additions & 10 deletions htslib/kseq.h
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Original file line number Diff line number Diff line change
Expand Up @@ -24,8 +24,6 @@
SOFTWARE.
*/

/* Last Modified: 05MAR2012 */

#ifndef AC_KSEQ_H
#define AC_KSEQ_H

Expand Down Expand Up @@ -57,6 +55,7 @@
unsigned char *buf; \
} 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 @@ -78,11 +77,13 @@
#define __KS_INLINED(__read) \
static inline klib_unused 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, ks->bufsize); \
if (ks->end == 0) { ks->is_eof = 1; return -1; } \
if (ks->end == -1) { ks->is_eof = 1; return -3; } \
} \
ks->seek_pos++; \
return (int)ks->buf[ks->begin++]; \
Expand All @@ -99,11 +100,13 @@
uint64_t seek_pos = str->l; \
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, ks->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 @@ -180,25 +183,27 @@
>=0 length of the sequence (normal)
-1 end-of-file
-2 truncated quality string
-3 error reading stream
-4 overflow error
*/
#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 @@ -207,7 +212,7 @@
if (seq->seq.l + 1 >= seq->seq.m) { /* seq->seq.s[seq->seq.l] below may be out of boundary */ \
seq->seq.m = seq->seq.l + 2; \
kroundup32(seq->seq.m); /* rounded to the next closest 2^k */ \
if (seq->seq.l + 1 >= seq->seq.m) return -3; /* error: adjusting m overflowed */ \
if (seq->seq.l + 1 >= seq->seq.m) return -4; /* error: adjusting m overflowed */ \
seq->seq.s = (char*)realloc(seq->seq.s, seq->seq.m); \
} \
seq->seq.s[seq->seq.l] = 0; /* null terminated string */ \
Expand All @@ -216,9 +221,10 @@
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