From 254280b8af11ef193adf83d7b77b9247d395e465 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Fri, 28 Jul 2017 11:54:18 -0400
Subject: [PATCH] r216: a bit cleanup; identical output to r215

---
 align.c  | 8 ++++----
 hit.c    | 2 +-
 main.c   | 2 +-
 map.c    | 5 ++++-
 mmpriv.h | 4 ++++
 5 files changed, 14 insertions(+), 7 deletions(-)

diff --git a/align.c b/align.c
index b515abd..9749b80 100644
--- a/align.c
+++ b/align.c
@@ -179,7 +179,7 @@ static void mm_filter_bad_seeds(void *km, int as1, int cnt1, mm128_t *a, int min
 		if (k == n || k >= max_en) {
 			if (max_en > 0)
 				for (i = K[max_st]; i < K[max_en]; ++i)
-					a[as1 + i].y |= 1ULL << 41;
+					a[as1 + i].y |= MM_SEED_IGNORE;
 			max = 0, max_st = max_en = -1;
 			if (k == n) break;
 		}
@@ -299,12 +299,12 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
 	assert(qs1 >= 0 && rs1 >= 0);
 
 	for (i = 1; i < cnt1; ++i) { // gap filling
-		if (a[as1+i].y>>41&1) continue;
+		if (a[as1+i].y & MM_SEED_IGNORE) continue;
 		mm_adjust_minier(mi, qseq0, &a[as1 + i], &re, &qe);
 		re1 = re, qe1 = qe;
-		if (i == cnt1 - 1 || (a[as1+i].y>>40&1) || qe - qs >= opt->min_ksw_len || re - rs >= opt->min_ksw_len) {
+		if (i == cnt1 - 1 || (a[as1+i].y&MM_SEED_LONG_JOIN) || qe - qs >= opt->min_ksw_len || re - rs >= opt->min_ksw_len) {
 			int bw1 = bw;
-			if (a[as1+i].y>>40&1)
+			if (a[as1+i].y & MM_SEED_LONG_JOIN)
 				bw1 = qe - qs > re - rs? qe - qs : re - rs;
 			qseq = &qseq0[rev][qs];
 			mm_idx_getseq(mi, rid, rs, re, tseq);
diff --git a/hit.c b/hit.c
index ba6bb76..e452d18 100644
--- a/hit.c
+++ b/hit.c
@@ -266,7 +266,7 @@ void mm_join_long(void *km, const mm_mapopt_t *opt, int qlen, int *n_regs_, mm_r
 		if (r1->re - r1->rs < max_gap>>1 || r1->qe - r1->qs < max_gap>>1) continue;
 
 		// all conditions satisfied; join
-		a[r1->as].y |= 1ULL<<40;
+		a[r1->as].y |= MM_SEED_LONG_JOIN;
 		r0->cnt += r1->cnt, r0->score += r1->score;
 		mm_reg_set_coor(r0, qlen, a);
 		r1->cnt = 0;
diff --git a/main.c b/main.c
index f5cc530..c7529aa 100644
--- a/main.c
+++ b/main.c
@@ -8,7 +8,7 @@
 #include "minimap.h"
 #include "mmpriv.h"
 
-#define MM_VERSION "2.0-r215-dirty"
+#define MM_VERSION "2.0-r216-dirty"
 
 void liftrlimit()
 {
diff --git a/map.c b/map.c
index 6a7d373..b3f3924 100644
--- a/map.c
+++ b/map.c
@@ -209,8 +209,10 @@ mm_reg1_t *mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b,
 		mm128_t *p = &b->mini.a[i + m_st];
 		mm_match_t *q = &m[i];
 		const uint64_t *r = q->x.cr;
-		int k, q_span = p->x & 0xff;
+		int k, q_span = p->x & 0xff, is_tandem = 0;
 		if (q->n >= opt->mid_occ) continue;
+		if (i > 0 && p->x>>8 == b->mini.a[m_st + i - 1].x>>8) is_tandem = 1;
+		if (i < n - 1 && p->x>>8 == b->mini.a[m_st + i + 1].x>>8) is_tandem = 1;
 		for (k = 0; k < q->n; ++k) {
 			const char *tname = mi->seq[r[k]>>32].name;
 			int32_t rpos = (uint32_t)r[k] >> 1;
@@ -227,6 +229,7 @@ mm_reg1_t *mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b,
 				p->x = 1ULL<<63 | (r[k]&0xffffffff00000000ULL) | (uint32_t)r[k]>>1;
 				p->y = (uint64_t)q_span << 32 | (qlen - ((q->qpos>>1) + 1 - q_span) - 1);
 			}
+			if (is_tandem) p->y |= MM_SEED_TANDEM;
 		}
 	}
 	n_a = j;
diff --git a/mmpriv.h b/mmpriv.h
index 6135172..dcf49ea 100644
--- a/mmpriv.h
+++ b/mmpriv.h
@@ -12,6 +12,10 @@
 #define MM_DBG_PRINT_QNAME 0x2
 #define MM_DBG_PRINT_SEED  0x4
 
+#define MM_SEED_LONG_JOIN  (1ULL<<40)
+#define MM_SEED_IGNORE     (1ULL<<41)
+#define MM_SEED_TANDEM     (1ULL<<42)
+
 #ifndef kroundup32
 #define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
 #endif