X-Git-Url: https://git.donarmstrong.com/?p=samtools.git;a=blobdiff_plain;f=kseq.h;h=a5cec7c289aeda5fe36edb2a828a9f669741d3a3;hp=0bbc7dc9370e910b19286167bd0862c64855387c;hb=307c147168f7154e3755712797078c513e0b242a;hpb=4efe4317c377019fbb64bcfae519403a3a9d1f5f

diff --git a/kseq.h b/kseq.h
index 0bbc7dc..a5cec7c 100644
--- a/kseq.h
+++ b/kseq.h
@@ -23,7 +23,7 @@
    SOFTWARE.
 */
 
-/* Last Modified: 18AUG2011 */
+/* 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 {				\
@@ -51,7 +52,7 @@
 	{																\
 		kstream_t *ks = (kstream_t*)calloc(1, sizeof(kstream_t));	\
 		ks->f = f;													\
-		ks->buf = malloc(__bufsize);								\
+		ks->buf = (unsigned char*)malloc(__bufsize);				\
 		return ks;													\
 	}																\
 	static inline void ks_destroy(kstream_t *ks)					\
@@ -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) {						\
@@ -113,7 +117,7 @@ typedef struct __kstring_t {
 				for (i = ks->begin; i < ks->end; ++i)					\
 					if (isspace(ks->buf[i]) && ks->buf[i] != ' ') break; \
 			} else i = 0; /* never come to here! */						\
-			if (str->m - str->l < i - ks->begin + 1) {					\
+			if (str->m - str->l < (size_t)(i - ks->begin + 1)) {		\
 				str->m = str->l + (i - ks->begin) + 1;					\
 				kroundup32(str->m);										\
 				str->s = (char*)realloc(str->s, str->m);				\
@@ -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;													\
 	} \
@@ -142,19 +146,16 @@ typedef struct __kstring_t {
 	__KS_GETC(__read, __bufsize)				\
 	__KS_GETUNTIL(__read, __bufsize)
 
-#define __KSEQ_BASIC(type_t)											\
-	static inline kseq_t *kseq_init(type_t fd)							\
+#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;														\
 	}																	\
-	static inline void kseq_rewind(kseq_t *ks)							\
-	{																	\
-		ks->last_char = 0;												\
-		ks->f->is_eof = ks->f->begin = ks->f->end = 0;					\
-	}																	\
-	static inline void kseq_destroy(kseq_t *ks)							\
+	SCOPE void kseq_destroy(kseq_t *ks)									\
 	{																	\
 		if (!ks) return;												\
 		free(ks->name.s); free(ks->comment.s); free(ks->seq.s);	free(ks->qual.s); \
@@ -167,8 +168,8 @@ typedef struct __kstring_t {
    -1   end-of-file
    -2   truncated quality string
  */
-#define __KSEQ_READ \
-	static int kseq_read(kseq_t *seq) \
+#define __KSEQ_READ(SCOPE) \
+	SCOPE int kseq_read(kseq_t *seq) \
 	{ \
 		int c; \
 		kstream_t *ks = seq->f; \
@@ -179,14 +180,15 @@ 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 != '@') { \
+			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, '\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 +204,7 @@ 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; \
@@ -215,10 +217,19 @@ typedef struct __kstring_t {
 		kstream_t *f;							\
 	} kseq_t;
 
-#define KSEQ_INIT(type_t, __read)				\
+#define KSEQ_INIT2(SCOPE, type_t, __read)		\
 	KSTREAM_INIT(type_t, __read, 16384)			\
 	__KSEQ_TYPE(type_t)							\
-	__KSEQ_BASIC(type_t)						\
-	__KSEQ_READ
+	__KSEQ_BASIC(SCOPE, type_t)					\
+	__KSEQ_READ(SCOPE)
+
+#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
+
+#define KSEQ_DECLARE(type_t) \
+	__KS_TYPE(type_t) \
+	__KSEQ_TYPE(type_t) \
+	extern kseq_t *kseq_init(type_t fd); \
+	void kseq_destroy(kseq_t *ks); \
+	int kseq_read(kseq_t *seq);
 
 #endif