r719: more stringent overlap merge

Will consider to make it the default

bwamem.c

@@ -371,28 +371,32 @@ int mem_sort_and_dedup2(int n, mem_alnreg_t *a, float mask_level_redun, int merg
 			int64_t or, oq, mr, mq;
 			int is_merged = 0;
 			if (q->qe == q->qb) continue; // a[j] has been excluded
-			if (merge_bw > 0 && q->qb < p->qb && q->qe < p->qe && q->re < p->re) {
+			or = q->re - p->rb; // overlap length on the reference
-				int flag = 0;
+			oq = q->qb < p->qb? q->qe - p->qb : p->qe - q->qb; // overlap length on the query
+			mr = q->re - q->rb < p->re - p->rb? q->re - q->rb : p->re - p->rb; // min ref len in alignment
+			mq = q->qe - q->qb < p->qe - p->qb? q->qe - q->qb : p->qe - p->qb; // min qry len in alignment
+			if (merge_bw > 0 && q->qb < p->qb && q->qe < p->qe && q->re < p->re && fabs((float)oq / (p->qe - q->qb) - (float)or / (p->re - q->rb)) < .05) {
+				int flag = 0, q_s, r_s;
 				int64_t l1, l2;
 				l1 = p->qb - q->qb, l2 = p->rb - q->rb;
 				if (l1 - l2 < merge_bw && l2 - l1 < merge_bw) ++flag;
 				l1 = p->qe - q->qe, l2 = p->re - q->re;
 				if (l1 - l2 < merge_bw && l2 - l1 < merge_bw) ++flag;
+				l1 = p->qe - q->qb, l2 = p->re - q->rb;
+				q_s = (int)((double)(p->qe - q->qb) / ((p->qe - p->qb) + (q->qe - q->qb)) * (p->score + q->score) + .499);
+				r_s = (int)((double)(p->re - q->rb) / ((p->re - p->rb) + (q->re - q->rb)) * (p->score + q->score) + .499);
 				if (flag == 2) { // merge q into p
 					mem_alnreg_t t = *p;
 					*p = *q;
 					p->qe = t.qe, p->re = t.re;
-					p->score = p->score > t.score? p->score : t.score;
+					p->truesc = p->score = (q_s + r_s) >> 1;
 					p->w = p->w > t.w? p->w : t.w;
+					p->w = p->w > abs(l1 - l2) + 50? p->w : abs(l1 - l2) + 50;
 					q->qb = q->qe;
 					is_merged = 1;
 				}
 			}
 			if (is_merged == 0) {
-				or = q->re - p->rb; // overlap length on the reference
-				oq = q->qb < p->qb? q->qe - p->qb : p->qe - q->qb; // overlap length on the query
-				mr = q->re - q->rb < p->re - p->rb? q->re - q->rb : p->re - p->rb; // min ref len in alignment
-				mq = q->qe - q->qb < p->qe - p->qb? q->qe - q->qb : p->qe - p->qb; // min qry len in alignment
 				if (or > mask_level_redun * mr && oq > mask_level_redun * mq) { // one of the hits is redundant
 					if (p->score < q->score) {
 						p->qe = p->qb;

main.c

@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.8-r718-dirty"
+#define PACKAGE_VERSION "0.7.8-r719-dirty"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);