  }
 diff -rupN -x Xcode -x .git bwa/bwamem.h bwa-mod/bwamem.h
 --- bwa/bwamem.h	2015-07-08 13:14:28.000000000 -0400
-+++ bwa-mod/bwamem.h	2015-08-06 16:18:00.000000000 -0400
-@@ -94,6 +94,9 @@ typedef struct { // This struct is only 
++++ bwa-mod/bwamem.h	2016-07-29 21:04:27.000000000 -0400
+@@ -94,6 +94,10 @@ typedef struct { // This struct is only 
  	char *XA;        // alternative mappings
  
  	int score, sub, alt_sc;
 +	float seedcov, pair_seedcov;
 +	int sub_n, pair_score, pair_sub, pair_nsub;
 +	float frac_rep, pair_frac_rep;
++	int seedlen0, n_comp;
  } mem_aln_t;
  
  #ifdef __cplusplus
-Binary files bwa/bwamem.o and bwa-mod/bwamem.o differ
-Binary files bwa/bwamem_extra.o and bwa-mod/bwamem_extra.o differ
 diff -rupN -x Xcode -x .git bwa/bwamem_pair.c bwa-mod/bwamem_pair.c
 --- bwa/bwamem_pair.c	2015-07-08 13:14:28.000000000 -0400
 +++ bwa-mod/bwamem_pair.c	2015-08-06 16:18:28.000000000 -0400

+		kputw(p->pair_score, str);
+		kputc(',', str);
+		if(p->pair_sub >= 0) {
+			//assert(p->pair_score >= p->pair_sub);
+			kputw(p->pair_score - p->pair_sub, str);
+		} else {
+			kputsn("NA", 2, str);
+		}
+		kputc(',', str);
+		kputw(p->sub_n, str);
+		kputc(',', str);

 	kputc('\n', str);
 }
 
@@ -1131,6 +1165,13 @@ mem_aln_t mem_reg2aln(const mem_opt_t *o
 	a.pos = pos - bns->anns[a.rid].offset;
 	a.score = ar->score; a.sub = ar->sub > ar->csub? ar->sub : ar->csub;
 	a.is_alt = ar->is_alt; a.alt_sc = ar->alt_sc;
+	a.seedlen0 = ar->seedlen0;
+	a.n_comp = ar->n_comp;
+	a.seedcov = ((float)ar->seedcov) / l_query;
+	a.frac_rep = ar->frac_rep;
+	a.sub_n = ar->sub_n;
