From 03d6894517ddf1cd29a6fd523839fa174c7d0b5b Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Wed, 20 Sep 2017 11:47:46 -0400
Subject: [PATCH] backup

---
 hit.c    | 14 +++++++++++++-
 map.c    |  2 +-
 mmpriv.h |  6 ++++++
 3 files changed, 20 insertions(+), 2 deletions(-)

diff --git a/hit.c b/hit.c
index d6e22a3..f775239 100644
--- a/hit.c
+++ b/hit.c
@@ -293,7 +293,19 @@ void mm_join_long(void *km, const mm_mapopt_t *opt, int qlen, int *n_regs_, mm_r
 		mm_sync_regs(km, *n_regs_, regs);
 	}
 }
-
+/*
+void mm_sep_seg(void *km, int n_segs, int qlen_sum, int n_regs0, mm_reg1_t *regs0, mm128_t *a, mm_segreg_t *seg)
+{ // TODO: this implement is inefficient given a large n_segs
+	int s, i, j;
+	memset(seg, 0, n_segs * sizeof(mm_segreg_t));
+	for (i = 0; i < n_regs0; ++i) {
+		mm_reg1_t *r = &regs0[i];
+		for (j = 0; j < r->cnt; ++j) {
+			++seg[(a[r->as + j].y&MM_SEED_SEG_MASK)>>MM_SEED_SEG_SHIFT].n_a;
+		}
+	}
+}
+*/
 void mm_set_mapq(int n_regs, mm_reg1_t *regs, int min_chain_sc, int match_sc, int rep_len)
 {
 	static const float q_coef = 40.0f;
diff --git a/map.c b/map.c
index 924e2dd..04dcfe6 100644
--- a/map.c
+++ b/map.c
@@ -268,7 +268,7 @@ mm_reg1_t *mm_map_seg(const mm_idx_t *mi, int n_segs, int *qlens, const char *se
 	if (!(opt->flag & MM_F_AVA)) { // don't choose primary mapping(s) for read overlap
 		mm_set_parent(b->km, opt->mask_level, *n_regs, regs, opt->a * 2 + opt->b);
 		mm_select_sub(b->km, opt->mask_level, opt->pri_ratio, mi->k*2, opt->best_n, n_regs, regs);
-		if (!(opt->flag & MM_F_SPLICE))
+		if (!(opt->flag & MM_F_SPLICE) && !(opt->flag & MM_F_SR))
 			mm_join_long(b->km, opt, qlen_sum, n_regs, regs, a); // TODO: this can be applied to all-vs-all in principle
 	}
 
diff --git a/mmpriv.h b/mmpriv.h
index 6830f65..19caa0a 100644
--- a/mmpriv.h
+++ b/mmpriv.h
@@ -39,6 +39,12 @@ typedef struct __kstring_t {
 } kstring_t;
 #endif
 
+typedef struct {
+	int n_regs, n_a;
+	mm_reg1_t *regs;
+	mm128_t *a;
+} mm_segreg_t;
+
 double cputime(void);
 double realtime(void);