compatibility with the Windows line separator

kseq.h

@@ -23,7 +23,7 @@
    SOFTWARE.
 */
 
-/* Last Modified: 29DEC2011 */
+/* Last Modified: 05MAR2012 */
 
 #ifndef AC_KSEQ_H
 #define AC_KSEQ_H
@@ -34,7 +34,8 @@
 
 #define KS_SEP_SPACE 0 // isspace(): \t, \n, \v, \f, \r
 #define KS_SEP_TAB   1 // isspace() && !' '
-#define KS_SEP_MAX   1
+#define KS_SEP_LINE  2 // line separator: "\n" (Unix) or "\r\n" (Windows)
+#define KS_SEP_MAX   2
 
 #define __KS_TYPE(type_t)						\
 	typedef struct __kstream_t {				\
@@ -103,7 +104,10 @@ typedef struct __kstring_t {
 					if (ks->end == 0) break;							\
 				} else break;											\
 			}															\
-			if (delimiter > KS_SEP_MAX) {								\
+			if (delimiter == KS_SEP_LINE) { \
+				for (i = ks->begin; i < ks->end; ++i) \
+					if (ks->buf[i] == '\n') break; \
+			} else if (delimiter > KS_SEP_MAX) {						\
 				for (i = ks->begin; i < ks->end; ++i)					\
 					if (ks->buf[i] == delimiter) break;					\
 			} else if (delimiter == KS_SEP_SPACE) {						\
@@ -129,7 +133,7 @@ typedef struct __kstring_t {
 		if (str->s == 0) {												\
 			str->m = 1;													\
 			str->s = (char*)calloc(1, 1);								\
-		}																\
+		} else if (delimiter == KS_SEP_LINE && str->l > 1 && str->s[str->l-1] == '\r') --str->l; \
 		str->s[str->l] = '\0';											\
 		return str->l;													\
 	} \
@@ -142,18 +146,15 @@ typedef struct __kstring_t {
 	__KS_GETC(__read, __bufsize)				\
 	__KS_GETUNTIL(__read, __bufsize)
 
+#define kseq_rewind(ks) ((ks)->last_char = (ks)->f->is_eof = (ks)->f->begin = (ks)->f->end = 0)
+
 #define __KSEQ_BASIC(SCOPE, type_t)										\
 	SCOPE kseq_t *kseq_init(type_t fd)									\
 	{																	\
 		kseq_t *s = (kseq_t*)calloc(1, sizeof(kseq_t));					\
 		s->f = ks_init(fd);												\
 		return s;														\
 	}																	\
-	SCOPE void kseq_rewind(kseq_t *ks)									\
-	{																	\
-		ks->last_char = 0;												\
-		ks->f->is_eof = ks->f->begin = ks->f->end = 0;					\
-	}																	\
 	SCOPE void kseq_destroy(kseq_t *ks)									\
 	{																	\
 		if (!ks) return;												\
@@ -179,14 +180,14 @@ typedef struct __kstring_t {
 		} /* 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 (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 != '@') { \
 			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 */ \
+			ks_getuntil2(ks, KS_SEP_LINE, &seq->seq, 0, 1); /* read the rest of the line */ \
 		} \
 		if (c == '>' || c == '@') seq->last_char = c; /* the first header char has been read */	\
 		if (seq->seq.l + 1 >= seq->seq.m) { /* seq->seq.s[seq->seq.l] below may be out of boundary */ \
@@ -202,7 +203,7 @@ typedef struct __kstring_t {
 		} \
 		while ((c = ks_getc(ks)) != -1 && c != '\n'); /* skip the rest of '+' line */ \
 		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); \
+		while (ks_getuntil2(ks, KS_SEP_LINE, &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; /* error: qual string is of a different length */ \
 		return seq->seq.l; \