X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=faidx.c;fp=faidx.c;h=6b4514ffa2f24946bdfed2228c8044cd8268e692;hb=9348942203fc319b5322d473726d1820341c6483;hp=9302dfb4d6480bb94295d65e7fc7fcf4c4644332;hpb=dcf3da39741a89592ab508e02b6f9969aa2aa951;p=samtools.git

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);