From: Heng Li <lh3@me.com>
Date: Sun, 15 Apr 2012 15:06:13 +0000 (-0400)
Subject: bugfix: empty fasta/q lines cause troubles
X-Git-Tag: spawn-final~54
X-Git-Url: http://www.kaiwu.me/postgresql/commit/static/gitweb.js?a=commitdiff_plain;h=37b020f9dbe913fa4ac4cdc402fb9b8c4b92ee96;p=klib.git

bugfix: empty fasta/q lines cause troubles
---

diff --git a/kseq.h b/kseq.h
index ab7f77f..a5cec7c 100644
--- a/kseq.h
+++ b/kseq.h
@@ -186,6 +186,7 @@ typedef struct __kstring_t {
 			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, KS_SEP_LINE, &seq->seq, 0, 1); /* read the rest of the line */ \
 		} \
@@ -217,7 +218,7 @@ typedef struct __kstring_t {
 	} kseq_t;
 
 #define KSEQ_INIT2(SCOPE, type_t, __read)		\
-	KSTREAM_INIT(type_t, __read, 4096)			\
+	KSTREAM_INIT(type_t, __read, 16384)			\
 	__KSEQ_TYPE(type_t)							\
 	__KSEQ_BASIC(SCOPE, type_t)					\
 	__KSEQ_READ(SCOPE)