From 9348942203fc319b5322d473726d1820341c6483 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@live.co.uk>
Date: Wed, 17 Jun 2009 23:16:26 +0000
Subject: [PATCH]  * samtools-0.1.4-13 (r351)  * make faidx more tolerant to
 empty lines right before or after > lines  * hope this does not introduce new
 bugs...

---
 bamtk.c | 2 +-
 faidx.c | 6 ++++++
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/bamtk.c b/bamtk.c
index b5afdf2..6c4626a 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -3,7 +3,7 @@
 #include "bam.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.4-13 (r350)"
+#define PACKAGE_VERSION "0.1.4-14 (r351)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);
diff --git a/faidx.c b/faidx.c
index 9302dfb..6b4514f 100644
--- a/faidx.c
+++ b/faidx.c
@@ -66,6 +66,12 @@ faidx_t *fai_build_core(RAZF *rz)
 	name = 0; l_name = m_name = 0;
 	len = line_len = line_blen = -1; state = 0; l1 = l2 = -1; offset = 0;
 	while (razf_read(rz, &c, 1)) {
+		if (c == '\n') { // an empty line
+			if (state == 1) {
+				offset = razf_tell(rz);
+				continue;
+			} else if ((state == 0 && len < 0) || state == 2) continue;
+		}
 		if (c == '>') { // fasta header
 			if (len >= 0)
 				fai_insert_index(idx, name, len, line_len, line_blen, offset);
-- 
2.39.5