From 5dcd8f8965ac704216ae484fdf47ec5185b7ed5f Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Fri, 30 Jun 2017 11:52:42 -0400
Subject: [PATCH] r117: fixed a bug in logic

---
 align.c | 5 +++--
 main.c  | 2 +-
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/align.c b/align.c
index 5b7ee6b..5723ba3 100644
--- a/align.c
+++ b/align.c
@@ -146,7 +146,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
 {
 	int32_t rid = a[r->as].x<<1>>33, rev = a[r->as].x>>63;
 	uint8_t *tseq, *qseq;
-	int32_t i, l, bw, rs0, re0, qs0, qe0;
+	int32_t i, l, bw, dropped = 0, rs0, re0, qs0, qe0;
 	int32_t rs, re, qs, qe;
 	int32_t rs1, qs1, re1, qe1;
 	int8_t mat[25];
@@ -229,6 +229,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
 				for (j = i - 1; j >= 0; --j)
 					if ((int32_t)a[r->as + j].x < re + ez->max_t)
 						break;
+				dropped = 1;
 				r->p->score += ez->max;
 				re1 = rs + (ez->max_t + 1);
 				qe1 = qs + (ez->max_q + 1);
@@ -245,7 +246,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
 		}
 	}
 
-	if (!r->split && qe < qe0 && re < re0) { // right extension
+	if (!dropped && qe < qe0 && re < re0) { // right extension
 		qseq = &qseq0[rev][qe];
 		mm_idx_getseq(mi, rid, re, re0, tseq);
 		ksw_extz2_sse(km, qe0 - qe, qseq, re0 - re, tseq, 5, mat, opt->q, opt->e, bw, opt->zdrop, KSW_EZ_EXTZ_ONLY, ez);
diff --git a/main.c b/main.c
index 598199b..5f95cc9 100644
--- a/main.c
+++ b/main.c
@@ -10,7 +10,7 @@
 #include "minimap.h"
 #include "mmpriv.h"
 
-#define MM_VERSION "2.0-r116-pre"
+#define MM_VERSION "2.0-r117-pre"
 
 void liftrlimit()
 {