From 28f86688ab962359d7c983abdd6a377fa3ace66b Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Sat, 12 Aug 2017 23:48:43 -0400
Subject: [PATCH] r295: gap closure from the middle of non-HPC k

This WILL slightly affect the result of genomic mapping, but hopefully
in the good direction.
---
 align.c | 4 ++--
 main.c  | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/align.c b/align.c
index 4f86ace..cca69cf 100644
--- a/align.c
+++ b/align.c
@@ -164,8 +164,8 @@ static inline void mm_adjust_minier(const mm_idx_t *mi, uint8_t *const qseq0[2],
 		c = mm_get_hplen_back(mi, a->x<<1>>33, (int32_t)a->x);
 		*r = (int32_t)a->x + 1 - c;
 	} else {
-		*r = (int32_t)a->x + 1;
-		*q = (int32_t)a->y + 1;
+		*r = (int32_t)a->x - (mi->k>>1);
+		*q = (int32_t)a->y - (mi->k>>1);
 	}
 }
 
diff --git a/main.c b/main.c
index 5722433..42dafd1 100644
--- a/main.c
+++ b/main.c
@@ -8,7 +8,7 @@
 #include "minimap.h"
 #include "mmpriv.h"
 
-#define MM_VERSION "2.0-r290-dirty"
+#define MM_VERSION "2.0-r295-dirty"
 
 void liftrlimit()
 {