  		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
+Binary files bwa/bwape.o and bwa-mod/bwape.o differ
+Binary files bwa/bwase.o and bwa-mod/bwase.o differ
+Binary files bwa/bwaseqio.o and bwa-mod/bwaseqio.o differ
+Binary files bwa/bwashm.o and bwa-mod/bwashm.o differ
+Binary files bwa/bwt.o and bwa-mod/bwt.o differ
+Binary files bwa/bwt_gen.o and bwa-mod/bwt_gen.o differ
+Binary files bwa/bwt_lite.o and bwa-mod/bwt_lite.o differ
+Binary files bwa/bwtaln.o and bwa-mod/bwtaln.o differ
+Binary files bwa/bwtgap.o and bwa-mod/bwtgap.o differ
+Binary files bwa/bwtindex.o and bwa-mod/bwtindex.o differ
+Binary files bwa/bwtsw2_aux.o and bwa-mod/bwtsw2_aux.o differ
+Binary files bwa/bwtsw2_chain.o and bwa-mod/bwtsw2_chain.o differ
+Binary files bwa/bwtsw2_core.o and bwa-mod/bwtsw2_core.o differ
+Binary files bwa/bwtsw2_main.o and bwa-mod/bwtsw2_main.o differ
+Binary files bwa/bwtsw2_pair.o and bwa-mod/bwtsw2_pair.o differ
+Binary files bwa/fastmap.o and bwa-mod/fastmap.o differ
+Binary files bwa/is.o and bwa-mod/is.o differ
+Binary files bwa/kopen.o and bwa-mod/kopen.o differ
+Binary files bwa/kstring.o and bwa-mod/kstring.o differ
+Binary files bwa/ksw.o and bwa-mod/ksw.o differ
+Binary files bwa/kthread.o and bwa-mod/kthread.o differ
+Binary files bwa/libbwa.a and bwa-mod/libbwa.a differ
+Binary files bwa/main.o and bwa-mod/main.o differ
+Binary files bwa/malloc_wrap.o and bwa-mod/malloc_wrap.o differ
+Binary files bwa/maxk.o and bwa-mod/maxk.o differ
+Binary files bwa/pemerge.o and bwa-mod/pemerge.o differ
+Binary files bwa/utils.o and bwa-mod/utils.o differ

 } mem_aln_t;
 
 #ifdef __cplusplus
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

 	kputc('\n', str);
 }
 
@@ -1131,6 +1164,11 @@ 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;
