60 #define ks_eof(ks) ((ks)->is_eof && (ks)->begin >= (ks)->end)  argument
61 #define ks_rewind(ks) ((ks)->is_eof = (ks)->begin = (ks)->end = 0)  argument
66 		kstream_t *ks = (kstream_t*)calloc(1, sizeof(kstream_t)); \
67 		ks->f = f; ks->bufsize = __bufsize; \
68 		ks->buf = (unsigned char*)malloc(__bufsize); \
69 		return ks; \
71 	SCOPE void ks_destroy(kstream_t *ks) \
73 		if (!ks) return; \
74 		free(ks->buf); \
75 		free(ks); \
79 	static inline klib_unused int ks_getc(kstream_t *ks) \
81 		if (ks->is_eof && ks->begin >= ks->end) return -1; \
82 		if (ks->begin >= ks->end) { \
83 			ks->begin = 0; \
84 			ks->end = __read(ks->f, ks->buf, ks->bufsize); \
85 			if (ks->end == 0) { ks->is_eof = 1; return -1; } \
87         ks->seek_pos++; \
88 		return (int)ks->buf[ks->begin++]; \
90 …static inline klib_unused int ks_getuntil(kstream_t *ks, int delimiter, kstring_t *str, int *dret)…
91 	{ return ks_getuntil2(ks, delimiter, str, dret, 0); }
94 	SCOPE int ks_getuntil2(kstream_t *ks, int delimiter, kstring_t *str, int *dret, int append)  \
102 			if (ks->begin >= ks->end) { \
103 				if (!ks->is_eof) { \
104 					ks->begin = 0; \
105 					ks->end = __read(ks->f, ks->buf, ks->bufsize); \
106 					if (ks->end == 0) { ks->is_eof = 1; break; } \
110 				for (i = ks->begin; i < ks->end; ++i)  \
111 					if (ks->buf[i] == '\n') break; \
113 				for (i = ks->begin; i < ks->end; ++i) \
114 					if (ks->buf[i] == delimiter) break; \
116 				for (i = ks->begin; i < ks->end; ++i) \
117 					if (isspace(ks->buf[i])) break; \
119 				for (i = ks->begin; i < ks->end; ++i) \
120 					if (isspace(ks->buf[i]) && ks->buf[i] != ' ') break;  \
122 			(void) ks_expand(str, i - ks->begin + 1); \
123             seek_pos += i - ks->begin; if ( i < ks->end ) seek_pos++; \
125 			memcpy(str->s + str->l, ks->buf + ks->begin, i - ks->begin);  \
126 			str->l = str->l + (i - ks->begin); \
127 			ks->begin = i + 1; \
128 			if (i < ks->end) { \
129 				if (dret) *dret = ks->buf[i]; \
133 		if (!gotany && ks_eof(ks)) return -1; \
134         ks->seek_pos += seek_pos; \
153 	extern int ks_getuntil2(kstream_t *ks, int delimiter, kstring_t *str, int *dret, int append); \
155 	extern void ks_destroy(kstream_t *ks); \
162 #define kseq_rewind(ks) ((ks)->last_char = (ks)->f->is_eof = (ks)->f->begin = (ks)->f->end = 0)  argument
171 	SCOPE void kseq_destroy(kseq_t *ks)									\
173 		if (!ks) return;												\
174 		free(ks->name.s); free(ks->comment.s); free(ks->seq.s);	free(ks->qual.s); \
175 		ks_destroy(ks->f);												\
176 		free(ks);														\
188 		kstream_t *ks = seq->f; \
190 			while ((c = ks_getc(ks)) != -1 && c != '>' && c != '@'); \
195 		if (ks_getuntil(ks, 0, &seq->name, &c) < 0) return -1; /* normal exit: EOF */ \
196 		if (c != '\n') ks_getuntil(ks, KS_SEP_LINE, &seq->comment, 0); /* read FASTA/Q comment */ \
201 		while ((c = ks_getc(ks)) != -1 && c != '>' && c != '+' && c != '@') { \
204 			ks_getuntil2(ks, KS_SEP_LINE, &seq->seq, 0, 1); /* read the rest of the line */ \
218 		while ((c = ks_getc(ks)) != -1 && c != '\n'); /* skip the rest of '+' line */ \
220 		while (ks_getuntil2(ks, KS_SEP_LINE, &seq->qual, 0, 1) >= 0 && seq->qual.l < seq->seq.l); \
245 	void kseq_destroy(kseq_t *ks); \