From c5fe18438a5b82d45cbce909cdd51a1c75fd9c64 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Thu, 13 Nov 2014 11:12:23 -0500
Subject: [PATCH] r984: updated to the latest kseq.h

---
 kseq.h | 18 +++++++++---------
 main.c |  2 +-
 2 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/kseq.h b/kseq.h
index 642cd33..f3862c6 100644
--- a/kseq.h
+++ b/kseq.h
@@ -54,9 +54,9 @@
 #define __KS_BASIC(type_t, __bufsize)								\
 	static inline kstream_t *ks_init(type_t f)						\
 	{																\
-		kstream_t *ks = (kstream_t*)calloc(1, sizeof(kstream_t)); \
+		kstream_t *ks = (kstream_t*)calloc(1, sizeof(kstream_t));	\
 		ks->f = f;													\
-		ks->buf = (unsigned char*)malloc(__bufsize);						\
+		ks->buf = (unsigned char*)malloc(__bufsize);				\
 		return ks;													\
 	}																\
 	static inline void ks_destroy(kstream_t *ks)					\
@@ -74,8 +74,7 @@
 		if (ks->begin >= ks->end) {							\
 			ks->begin = 0;									\
 			ks->end = __read(ks->f, ks->buf, __bufsize);	\
-			if (ks->end < __bufsize) ks->is_eof = 1;		\
-			if (ks->end == 0) return -1;					\
+			if (ks->end == 0) { ks->is_eof = 1; return -1;}	\
 		}													\
 		return (int)ks->buf[ks->begin++];					\
 	}
@@ -95,17 +94,16 @@ typedef struct __kstring_t {
 #define __KS_GETUNTIL(__read, __bufsize)								\
 	static int ks_getuntil2(kstream_t *ks, int delimiter, kstring_t *str, int *dret, int append) \
 	{																	\
+		int gotany = 0;													\
 		if (dret) *dret = 0;											\
 		str->l = append? str->l : 0;									\
-		if (ks->begin >= ks->end && ks->is_eof) return -1;				\
 		for (;;) {														\
 			int i;														\
 			if (ks->begin >= ks->end) {									\
 				if (!ks->is_eof) {										\
 					ks->begin = 0;										\
 					ks->end = __read(ks->f, ks->buf, __bufsize);		\
-					if (ks->end < __bufsize) ks->is_eof = 1;			\
-					if (ks->end == 0) break;							\
+					if (ks->end == 0) { ks->is_eof = 1; break; }		\
 				} else break;											\
 			}															\
 			if (delimiter == KS_SEP_LINE) { \
@@ -124,8 +122,9 @@ typedef struct __kstring_t {
 			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);			\
+				str->s = (char*)realloc(str->s, str->m);				\
 			}															\
+			gotany = 1;													\
 			memcpy(str->s + str->l, ks->buf + ks->begin, i - ks->begin); \
 			str->l = str->l + (i - ks->begin);							\
 			ks->begin = i + 1;											\
@@ -134,6 +133,7 @@ typedef struct __kstring_t {
 				break;													\
 			}															\
 		}																\
+		if (!gotany && ks_eof(ks)) return -1;							\
 		if (str->s == 0) {												\
 			str->m = 1;													\
 			str->s = (char*)calloc(1, 1);								\
@@ -155,7 +155,7 @@ typedef struct __kstring_t {
 #define __KSEQ_BASIC(SCOPE, type_t)										\
 	SCOPE kseq_t *kseq_init(type_t fd)									\
 	{																	\
-		kseq_t *s = (kseq_t*)calloc(1, sizeof(kseq_t));				\
+		kseq_t *s = (kseq_t*)calloc(1, sizeof(kseq_t));					\
 		s->f = ks_init(fd);												\
 		return s;														\
 	}																	\
diff --git a/main.c b/main.c
index f5448d7..33e27c2 100644
--- a/main.c
+++ b/main.c
@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.10-r983-dirty"
+#define PACKAGE_VERSION "0.7.10-r984-dirty"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);