From 6db2fd98aae29fcff3dae469c7672c756fc7fff3 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Tue, 28 Oct 2014 13:46:40 -0400
Subject: [PATCH] r960: merge changes from the master branch

---
 bwa-postalt.js |  4 +++-
 bwamem_pair.c  | 14 +++++++-------
 main.c         |  2 +-
 3 files changed, 11 insertions(+), 9 deletions(-)

diff --git a/bwa-postalt.js b/bwa-postalt.js
index b538552..6cf3dc7 100644
--- a/bwa-postalt.js
+++ b/bwa-postalt.js
@@ -577,11 +577,12 @@ function bwa_postalt(args)
 
 		// stage the hits generated from the XA tag
 		var cnt = 0;
+		var rg = (m = /\t(RG:Z:\S+)/.exec(line)) != null? m[1] : null;
 		for (var i = 0; i < hits.length; ++i) {
 			if (opt.verbose >= 5) print(obj2str(hits[i]));
 			if (hits[i].g != reported_g || i == reported_i) continue;
 			if (!opt.show_pri && idx_alt[hits[i].ctg] == null) continue;
-			var s = [t[0], 0, hits[i].ctg, hits[i].start+1, mapQ, hits[i].cigar, '*', 0, 0];
+			var s = [t[0], 0, hits[i].ctg, hits[i].start+1, mapQ, hits[i].cigar, t[6], t[7], t[8]];
 			// print sequence/quality and set the rev flag
 			if (hits[i].rev == hits[reported_i].rev) {
 				s.push(t[9], t[10]);
@@ -592,6 +593,7 @@ function bwa_postalt(args)
 			}
 			s.push("NM:i:" + hits[i].NM);
 			if (hits[i].lifted_str) s.push("lt:Z:" + hits[i].lifted_str);
+			if (rg != null) s.push(rg);
 			buf2.push(s);
 		}
 	}
diff --git a/bwamem_pair.c b/bwamem_pair.c
index 5d4c5c2..e405423 100644
--- a/bwamem_pair.c
+++ b/bwamem_pair.c
@@ -327,13 +327,13 @@ int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, co
 		// suboptimal hits
 		if (!(opt->flag & MEM_F_ALL)) {
 			for (i = 0; i < 2; ++i) {
-				int k = a[i].a[z[i]].secondary;
-				if (k >= 0) { // switch secondary and primary
-					assert(a[i].a[k].secondary < 0);
-					for (j = 0; j < n_pri[i]; ++j)
-						if (a[i].a[j].secondary == k || j == k)
-							a[i].a[j].secondary = z[i];
-					a[i].a[z[i]].secondary = -1;
+				int k = a[i].a[z[i]].secondary_all;
+				if (k >= 0 && k < n_pri[i]) { // switch secondary and primary if both of them are non-ALT
+					assert(a[i].a[k].secondary_all < 0);
+					for (j = 0; j < a[i].n; ++j)
+						if (a[i].a[j].secondary_all == k || j == k)
+							a[i].a[j].secondary_all = z[i];
+					a[i].a[z[i]].secondary_all = -1;
 				}
 				XA[i] = mem_gen_alt(opt, bns, pac, &a[i], s[i].l_seq, s[i].seq);
 			}
diff --git a/main.c b/main.c
index 7591875..f8f6995 100644
--- a/main.c
+++ b/main.c
@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.10-r943-dirty"
+#define PACKAGE_VERSION "0.7.10-r960-dirty"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);