/* The MIT License
- Copyright (c) 2008 Genome Research Ltd (GRL).
+ Copyright (c) 2008, 2009, 2011 Attractive Chaos <attractor@live.co.uk>
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
SOFTWARE.
*/
-/* Contact: Heng Li <lh3@sanger.ac.uk> */
-
-/*
- 2009-07-16 (lh3): in kstream_t, change "char*" to "unsigned char*"
- */
-
-/* Last Modified: 12APR2009 */
+/* Last Modified: 18AUG2011 */
#ifndef AC_KSEQ_H
#define AC_KSEQ_H
#endif
#define __KS_GETUNTIL(__read, __bufsize) \
- static int ks_getuntil(kstream_t *ks, int delimiter, kstring_t *str, int *dret) \
+ static int ks_getuntil2(kstream_t *ks, int delimiter, kstring_t *str, int *dret, int append) \
{ \
if (dret) *dret = 0; \
- str->l = 0; \
+ str->l = append? str->l : 0; \
if (ks->begin >= ks->end && ks->is_eof) return -1; \
for (;;) { \
int i; \
break; \
} \
} \
- if (str->l == 0) { \
+ if (str->s == 0) { \
str->m = 1; \
str->s = (char*)calloc(1, 1); \
} \
str->s[str->l] = '\0'; \
return str->l; \
- }
+ } \
+ static inline int ks_getuntil(kstream_t *ks, int delimiter, kstring_t *str, int *dret) \
+ { return ks_getuntil2(ks, delimiter, str, dret, 0); }
#define KSTREAM_INIT(type_t, __read, __bufsize) \
__KS_TYPE(type_t) \
-1 end-of-file
-2 truncated quality string
*/
-#define __KSEQ_READ \
- static int kseq_read(kseq_t *seq) \
- { \
- int c; \
- kstream_t *ks = seq->f; \
+#define __KSEQ_READ \
+ static int kseq_read(kseq_t *seq) \
+ { \
+ int c; \
+ 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 */ \
- seq->last_char = c; \
- } /* the first header char has been read */ \
- seq->comment.l = seq->seq.l = seq->qual.l = 0; \
- if (ks_getuntil(ks, 0, &seq->name, &c) < 0) return -1; \
- if (c != '\n') ks_getuntil(ks, '\n', &seq->comment, 0); \
+ while ((c = ks_getc(ks)) != -1 && c != '>' && c != '@'); \
+ if (c == -1) return -1; /* end of file */ \
+ 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 (c != '\n') ks_getuntil(ks, '\n', &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 != '@') { \
- if (isgraph(c)) { /* printable non-space character */ \
- if (seq->seq.l + 1 >= seq->seq.m) { /* double the memory */ \
- seq->seq.m = seq->seq.l + 2; \
- kroundup32(seq->seq.m); /* rounded to next closest 2^k */ \
- seq->seq.s = (char*)realloc(seq->seq.s, seq->seq.m); \
- } \
- seq->seq.s[seq->seq.l++] = (char)c; \
- } \
- } \
+ seq->seq.s[seq->seq.l++] = c; /* this is safe: we always have enough space for 1 char */ \
+ ks_getuntil2(ks, '\n', &seq->seq, 0, 1); /* read the rest of the line */ \
+ } \
if (c == '>' || c == '@') seq->last_char = c; /* the first header char has been read */ \
- seq->seq.s[seq->seq.l] = 0; /* null terminated string */ \
- if (c != '+') return seq->seq.l; /* FASTA */ \
- if (seq->qual.m < seq->seq.m) { /* allocate enough memory */ \
- seq->qual.m = seq->seq.m; \
- seq->qual.s = (char*)realloc(seq->qual.s, seq->qual.m); \
- } \
+ 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 */ \
+ seq->seq.s = (char*)realloc(seq->seq.s, seq->seq.m); \
+ } \
+ seq->seq.s[seq->seq.l] = 0; /* null terminated string */ \
+ if (c != '+') return seq->seq.l; /* FASTA */ \
+ if (seq->qual.m < seq->seq.m) { /* allocate memory for qual in case insufficient */ \
+ 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 */ \
- if (c == -1) return -2; /* we should not stop here */ \
- while ((c = ks_getc(ks)) != -1 && seq->qual.l < seq->seq.l) \
- if (c >= 33 && c <= 127) seq->qual.s[seq->qual.l++] = (unsigned char)c; \
- seq->qual.s[seq->qual.l] = 0; /* null terminated string */ \
+ if (c == -1) return -2; /* error: no quality string */ \
+ while (ks_getuntil2(ks, '\n', &seq->qual, 0, 1) >= 0 && seq->qual.l < seq->seq.l); \
seq->last_char = 0; /* we have not come to the next header line */ \
- if (seq->seq.l != seq->qual.l) return -2; /* qual string is shorter than seq string */ \
- return seq->seq.l; \
+ if (seq->seq.l != seq->qual.l) return -2; /* error: qual string is of a different length */ \
+ return seq->seq.l; \
}
#define __KSEQ_TYPE(type_t) \
} kseq_t;
#define KSEQ_INIT(type_t, __read) \
- KSTREAM_INIT(type_t, __read, 4096) \
+ KSTREAM_INIT(type_t, __read, 16384) \
__KSEQ_TYPE(type_t) \
__KSEQ_BASIC(type_t) \
__KSEQ_READ
projects / samtools.git / blobdiff