From e8f28cb5298b30c251446abd1fed67ce96cc5845 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Fri, 2 May 2014 16:17:50 -0400
Subject: [PATCH] r747: fixed a minor issue in the last (mis)commit

---
 bwamem.c | 4 ++--
 main.c   | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/bwamem.c b/bwamem.c
index 5fb41f8..7ac9bf8 100644
--- a/bwamem.c
+++ b/bwamem.c
@@ -248,11 +248,11 @@ mem_chain_v mem_chain(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *bn
 	l_rep += e - b;
 	for (i = 0; i < aux->mem.n; ++i) {
 		bwtintv_t *p = &aux->mem.a[i];
-		int step, slen = (uint32_t)p->info - (p->info>>32); // seed length
+		int step, count, slen = (uint32_t)p->info - (p->info>>32); // seed length
 		int64_t k;
 		if (slen < opt->min_seed_len) continue; // ignore if too short or too repetitive
 		step = p->x[2] > opt->max_occ? p->x[2] / opt->max_occ : 1;
-		for (k = 0; k < p->x[2]; k += step) {
+		for (k = count = 0; k < p->x[2] && count < opt->max_occ; k += step, ++count) {
 			mem_chain_t tmp, *lower, *upper;
 			mem_seed_t s;
 			int rid, to_add = 0;
diff --git a/main.c b/main.c
index bbeda8e..aa210dd 100644
--- a/main.c
+++ b/main.c
@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.8-r746-dirty"
+#define PACKAGE_VERSION "0.7.8-r747-dirty"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);