From 3c038250f94194b6c9515ba9ae3de9ca6c177563 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Thu, 28 Apr 2016 15:39:18 -0400
Subject: [PATCH] r1130: changed "ah" to "AH"

---
 bwa.c  | 7 +++++--
 main.c | 2 +-
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/bwa.c b/bwa.c
index f9ce6a1..c8dd015 100644
--- a/bwa.c
+++ b/bwa.c
@@ -379,8 +379,11 @@ void bwa_print_sam_hdr(const bntseq_t *bns, const char *hdr_line)
 		}
 	}
 	if (n_SQ == 0) {
-		for (i = 0; i < bns->n_seqs; ++i)
-			err_printf("@SQ\tSN:%s\tLN:%d\n", bns->anns[i].name, bns->anns[i].len);
+		for (i = 0; i < bns->n_seqs; ++i) {
+			err_printf("@SQ\tSN:%s\tLN:%d", bns->anns[i].name, bns->anns[i].len);
+			if (bns->anns[i].is_alt) err_printf("\tAH:Y\n");
+			else err_fputc('\n', stdout);
+		}
 	} else if (n_SQ != bns->n_seqs && bwa_verbose >= 2)
 		fprintf(stderr, "[W::%s] %d @SQ lines provided with -H; %d sequences in the index. Continue anyway.\n", __func__, n_SQ, bns->n_seqs);
 	if (hdr_line) err_printf("%s\n", hdr_line);
diff --git a/main.c b/main.c
index a5ae5fa..e17da14 100644
--- a/main.c
+++ b/main.c
@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.13-r1126"
+#define PACKAGE_VERSION "0.7.13-r1130-dirty"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);