-Binary files bwa/QSufSort.o and bwa-mod/QSufSort.o differ
-Binary files bwa/bamlite.o and bwa-mod/bamlite.o differ
-Binary files bwa/bntseq.o and bwa-mod/bntseq.o differ
-Binary files bwa/bwa and bwa-mod/bwa differ
-Binary files bwa/bwa.o and bwa-mod/bwa.o differ
 diff -rupN -x Xcode -x .git bwa/bwamem.c bwa-mod/bwamem.c
 --- bwa/bwamem.c	2015-07-08 13:14:28.000000000 -0400
-+++ bwa-mod/bwamem.c	2015-08-28 15:12:12.000000000 -0400
-@@ -942,6 +942,39 @@ void mem_aln2sam(const mem_opt_t *opt, c
++++ bwa-mod/bwamem.c	2016-07-29 21:32:26.000000000 -0400
+@@ -942,6 +942,40 @@ void mem_aln2sam(const mem_opt_t *opt, c
  		for (i = tmp; i < str->l; ++i) // replace TAB in the comment to SPACE
  			if (str->s[i] == '\t') str->s[i] = ' ';
  	}
 +	if ((p->flag & 4) == 0) {
 +		kputsn("\tZT:Z:", 6, str);
-+		//kputs((char*)(p->cigar + p->n_cigar), str);
-+		//kputc(',', str);
 +		kputw(p->score, str); // same as AS:i
 +		kputc(',', str);
 +		if(p->sub >= 0) {

 		for (i = 0; i < n_aa[0]; ++i)
 			mem_aln2sam(opt, bns, &str, &s[0], n_aa[0], aa[0], i, &h[1]); // write read1 hits
 		s[0].sam = strdup(str.s); str.l = 0;
Binary files bwa/bwamem_pair.o and bwa-mod/bwamem_pair.o differ
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Binary files bwa/bwtsw2_core.o and bwa-mod/bwtsw2_core.o differ
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 	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;
