From 935a6e6064411ae55da88d9fcfccab78434e4c67 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Wed, 27 Sep 2017 23:51:05 -0400
Subject: [PATCH] r450: differentiate exact repeats via mapq

---
 hit.c  | 1 +
 main.c | 2 +-
 pe.c   | 7 +++++++
 3 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/hit.c b/hit.c
index 4d98847..111ec27 100644
--- a/hit.c
+++ b/hit.c
@@ -383,6 +383,7 @@ void mm_set_mapq(int n_regs, mm_reg1_t *regs, int min_chain_sc, int match_sc, in
 			mapq -= (int)(4.343f * logf(r->n_sub + 1) + .499f);
 			mapq = mapq > 0? mapq : 0;
 			r->mapq = mapq < 60? mapq : 60;
+			if (r->p && r->p->dp_max > r->p->dp_max2 && r->mapq == 0) r->mapq = 1;
 		} else r->mapq = 0;
 	}
 }
diff --git a/main.c b/main.c
index 17b7b11..c525f8c 100644
--- a/main.c
+++ b/main.c
@@ -6,7 +6,7 @@
 #include "mmpriv.h"
 #include "getopt.h"
 
-#define MM_VERSION "2.2-r448-dirty"
+#define MM_VERSION "2.2-r450-dirty"
 
 #ifdef __linux__
 #include <sys/resource.h>
diff --git a/pe.c b/pe.c
index f74dddd..bdf16b1 100644
--- a/pe.c
+++ b/pe.c
@@ -135,6 +135,13 @@ void mm_pair(void *km, int max_gap_ref, int pe_bonus, int sub_diff, int match_sc
 		}
 		if (r[0]->mapq < mapq_pe) r[0]->mapq = (r[0]->mapq + mapq_pe) / 2;
 		if (r[1]->mapq < mapq_pe) r[1]->mapq = (r[1]->mapq + mapq_pe) / 2;
+		if (sc.n == 1) {
+			if (r[0]->mapq < 2) r[0]->mapq = 2;
+			if (r[1]->mapq < 2) r[1]->mapq = 2;
+		} else if (max > sc.a[sc.n - 2]) {
+			if (r[0]->mapq < 1) r[0]->mapq = 1;
+			if (r[1]->mapq < 1) r[1]->mapq = 1;
+		}
 	}
 
 	kfree(km, a);