From f4fee60188b694e79da405ed22ecfd6086154d10 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Fri, 28 Jul 2017 12:26:56 -0400
Subject: [PATCH] r217: ignore tandem seeds during alignment

This helps a tiny bit.
---
 align.c | 2 +-
 main.c  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/align.c b/align.c
index 9749b80..192c6c7 100644
--- a/align.c
+++ b/align.c
@@ -299,7 +299,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
 	assert(qs1 >= 0 && rs1 >= 0);
 
 	for (i = 1; i < cnt1; ++i) { // gap filling
-		if (a[as1+i].y & MM_SEED_IGNORE) continue;
+		if (a[as1+i].y & (MM_SEED_IGNORE|MM_SEED_TANDEM)) continue;
 		mm_adjust_minier(mi, qseq0, &a[as1 + i], &re, &qe);
 		re1 = re, qe1 = qe;
 		if (i == cnt1 - 1 || (a[as1+i].y&MM_SEED_LONG_JOIN) || qe - qs >= opt->min_ksw_len || re - rs >= opt->min_ksw_len) {
diff --git a/main.c b/main.c
index c7529aa..fc67289 100644
--- a/main.c
+++ b/main.c
@@ -8,7 +8,7 @@
 #include "minimap.h"
 #include "mmpriv.h"
 
-#define MM_VERSION "2.0-r216-dirty"
+#define MM_VERSION "2.0-r217-dirty"
 
 void liftrlimit()
 {