From 858213d513a9279364b8b6cfc87f233f6a888b85 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Thu, 12 Oct 2017 23:02:18 -0400
Subject: [PATCH] r511: fixed wrong primary sam record

---
 main.c | 2 +-
 map.c  | 2 +-
 pe.c   | 9 ++++++---
 3 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/main.c b/main.c
index d1619b7..316c9ce 100644
--- a/main.c
+++ b/main.c
@@ -6,7 +6,7 @@
 #include "mmpriv.h"
 #include "getopt.h"
 
-#define MM_VERSION "2.2-r510-dirty"
+#define MM_VERSION "2.2-r511-dirty"
 
 #ifdef __linux__
 #include <sys/resource.h>
diff --git a/map.c b/map.c
index 27c5818..fb291b6 100644
--- a/map.c
+++ b/map.c
@@ -306,7 +306,7 @@ void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **
 
 	a = mm_chain_dp(max_chain_gap_ref, max_chain_gap_qry, opt->bw, opt->max_chain_skip, opt->min_cnt, opt->min_chain_score, is_splice, n_segs, n_a, a, &n_regs0, &u, b->km);
 
-	if ((opt->flag & MM_F_SR) && rep_len > 0) {
+	if (opt->max_occ > opt->mid_occ && rep_len > 0) {
 		int rechain = 0;
 		if (n_regs0 > 0) { // test if the best chain has all the segments
 			int n_chained_segs = 1, max = 0, max_i = -1, max_off = -1, off = 0;
diff --git a/pe.c b/pe.c
index 70affcc..a1f9fda 100644
--- a/pe.c
+++ b/pe.c
@@ -117,13 +117,18 @@ void mm_pair(void *km, int max_gap_ref, int pe_bonus, int sub_diff, int match_sc
 		r[0] = a[max_idx[0]].r, r[1] = a[max_idx[1]].r;
 		r[0]->proper_frag = r[1]->proper_frag = 1;
 		for (s = 0; s < 2; ++s) {
-			if (r[s]->id != r[s]->parent) {
+			if (r[s]->id != r[s]->parent) { // then lift to primary and update parent
 				mm_reg1_t *p = &regs[s][r[s]->parent];
 				for (i = 0; i < n_regs[s]; ++i)
 					if (regs[s][i].parent == p->id)
 						regs[s][i].parent = r[s]->id;
 				p->mapq = 0;
 			}
+			if (!r[s]->sam_pri) { // then sync sam_pri
+				for (i = 0; i < n_regs[s]; ++i)
+					regs[s][i].sam_pri = 0;
+				r[s]->sam_pri = 1;
+			}
 		}
 		mapq_pe = r[0]->mapq > r[1]->mapq? r[0]->mapq : r[1]->mapq;
 		for (i = 0; i < sc.n; ++i)
@@ -144,8 +149,6 @@ void mm_pair(void *km, int max_gap_ref, int pe_bonus, int sub_diff, int match_sc
 			if (r[1]->mapq < 1) r[1]->mapq = 1;
 		}
 	}
-	mm_set_sam_pri(n_regs[0], regs[0]);
-	mm_set_sam_pri(n_regs[1], regs[1]);
 
 	kfree(km, a);
 	kfree(km, sc.a);