From dbf284b2d926fc8ddb0d4a484b1ac21bea7f3a56 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Mon, 5 Feb 2018 11:40:38 -0500
Subject: [PATCH] r684: separate end score from min_chain_score

---
 align.c           | 6 +++---
 main.c            | 2 +-
 minimap.h         | 1 +
 misc/mapstat.js   | 2 ++
 options.c         | 1 +
 python/cmappy.pxd | 1 +
 6 files changed, 9 insertions(+), 4 deletions(-)
 mode change 100644 => 100755 misc/mapstat.js

diff --git a/align.c b/align.c
index f096bae..a6d4817 100644
--- a/align.c
+++ b/align.c
@@ -307,7 +307,7 @@ static void mm_fix_bad_ends(const mm_reg1_t *r, const mm128_t *a, int bw, int mi
 		if (max - min > l >> 1) *as = i;
 		l += min;
 		m += min < q_span? min : q_span;
-		if (l >= bw << 1 || m >= min_match) break;
+		if (l >= bw << 1 || m >= min_match || m >= r->mlen >> 1) break;
 	}
 	*cnt = r->as + r->cnt - *as;
 	m = l = a[r->as + r->cnt - 1].y >> 32 & 0xff;
@@ -321,7 +321,7 @@ static void mm_fix_bad_ends(const mm_reg1_t *r, const mm128_t *a, int bw, int mi
 		if (max - min > l >> 1) *cnt = i + 1 - *as;
 		l += min;
 		m += min < q_span? min : q_span;
-		if (l >= bw << 1 || m >= min_match) break;
+		if (l >= bw << 1 || m >= min_match || m >= r->mlen >> 1) break;
 	}
 }
 
@@ -422,7 +422,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
 		if (is_splice) {
 			mm_fix_bad_ends_splice(km, opt, mi, r, mat, qlen, qseq0, a, &as1, &cnt1);
 		} else {
-			mm_fix_bad_ends(r, a, opt->bw, opt->min_chain_score, &as1, &cnt1);
+			mm_fix_bad_ends(r, a, opt->bw, opt->min_end_match, &as1, &cnt1);
 		}
 		mm_filter_bad_seeds(km, as1, cnt1, a, 10, 40, opt->max_gap>>1, 10);
 		mm_adjust_minier(mi, qseq0, &a[as1], &rs, &qs);
diff --git a/main.c b/main.c
index f45655f..1bc34b1 100644
--- a/main.c
+++ b/main.c
@@ -6,7 +6,7 @@
 #include "mmpriv.h"
 #include "getopt.h"
 
-#define MM_VERSION "2.8-r677-dirty"
+#define MM_VERSION "2.8-r684-dirty"
 
 #ifdef __linux__
 #include <sys/resource.h>
diff --git a/minimap.h b/minimap.h
index 6907387..333c188 100644
--- a/minimap.h
+++ b/minimap.h
@@ -120,6 +120,7 @@ typedef struct {
 	int end_bonus;
 	int min_dp_max;  // drop an alignment if the score of the max scoring segment is below this threshold
 	int min_ksw_len;
+	int min_end_match;
 	int anchor_ext_len, anchor_ext_shift;
 
 	int pe_ori, pe_bonus;
diff --git a/misc/mapstat.js b/misc/mapstat.js
old mode 100644
new mode 100755
index 98e42c3..4a11851
--- a/misc/mapstat.js
+++ b/misc/mapstat.js
@@ -1,3 +1,5 @@
+#!/usr/bin/env k8
+
 var getopt = function(args, ostr) {
 	var oli; // option letter list index
 	if (typeof(getopt.place) == 'undefined')
diff --git a/options.c b/options.c
index 4b67ab2..e202a67 100644
--- a/options.c
+++ b/options.c
@@ -28,6 +28,7 @@ void mm_mapopt_init(mm_mapopt_t *opt)
 	opt->end_bonus = -1;
 	opt->min_dp_max = opt->min_chain_score * opt->a;
 	opt->min_ksw_len = 200;
+	opt->min_end_match = 200;
 	opt->anchor_ext_len = 20, opt->anchor_ext_shift = 6;
 	opt->mini_batch_size = 500000000;
 
diff --git a/python/cmappy.pxd b/python/cmappy.pxd
index 6d1b931..de7f5f0 100644
--- a/python/cmappy.pxd
+++ b/python/cmappy.pxd
@@ -30,6 +30,7 @@ cdef extern from "minimap.h":
 		int end_bonus
 		int min_dp_max
 		int min_ksw_len
+		int min_end_match;
 		int anchor_ext_len, anchor_ext_shift
 		int pe_ori, pe_bonus
 		float mid_occ_frac