From e61812ee556bed1969a5f016191d72dc5e9ec409 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Tue, 1 May 2018 16:17:21 -0400
Subject: [PATCH] reduced gap len to trigger bad seed filtering

---
 align.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/align.c b/align.c
index 8e62a4c..ae58ef2 100644
--- a/align.c
+++ b/align.c
@@ -495,7 +495,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
 			mm_fix_bad_ends(r, a, opt->bw, opt->min_chain_score * 2, &as1, &cnt1);
 		}
 		mm_filter_bad_seeds(km, as1, cnt1, a, 10, 40, opt->max_gap>>1, 10);
-		mm_filter_bad_seeds_alt(km, as1, cnt1, a, 50);
+		mm_filter_bad_seeds_alt(km, as1, cnt1, a, 30);
 		mm_adjust_minier(mi, qseq0, &a[as1], &rs, &qs);
 		mm_adjust_minier(mi, qseq0, &a[as1 + cnt1 - 1], &re, &qe);
 	}