From 3370ae9e358a9fc75b12b44eb3fee746cfe0ebc8 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Sun, 19 Oct 2014 20:43:53 -0400
Subject: [PATCH] r926: prepare to move -g to bwa-postalt.js

---
 bwa-postalt.js | 11 +++++++----
 bwamem.c       |  2 +-
 main.c         |  2 +-
 3 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/bwa-postalt.js b/bwa-postalt.js
index 411cfdd..47c4847 100644
--- a/bwa-postalt.js
+++ b/bwa-postalt.js
@@ -490,13 +490,16 @@ function bwa_postalt(args)
 				while ((m = re_cigar.exec(t[5])) != null)
 					if (m[2] == 'M' || m[2] == 'D' || m[2] == 'N')
 						end += parseInt(m[1]);
+				var om = -1;
+				for (var j = 11; j < s.length; ++j)
+					if ((m = /^om:i:(\d+)/.exec(s[j])) != null)
+						om = parseInt(m[1]);
 				if (start < l[3] && l[2] < end) {
-					var om = -1;
-					for (var j = 11; j < s.length; ++j)
-						if ((m = /^om:i:(\d+)/.exec(s[j])) != null)
-							om = parseInt(m[1]);
 					if (om > 0) s[4] = om;
 					s[4] = s[4] < mapQ? s[4] : mapQ;
+				} else {
+					if (om < 0) s.push("om:i:" + s[4]);
+					s[4] = 0;
 				}
 			}
 		}
diff --git a/bwamem.c b/bwamem.c
index 79785f4..08588d5 100644
--- a/bwamem.c
+++ b/bwamem.c
@@ -79,7 +79,7 @@ mem_opt_t *mem_opt_init()
 	o->min_chain_weight = 0;
 	o->max_chain_extend = 1<<30;
 	o->mapQ_coef_len = 50; o->mapQ_coef_fac = log(o->mapQ_coef_len);
-	o->min_pa_ratio = 0.8;
+	o->min_pa_ratio = 0;
 	bwa_fill_scmat(o->a, o->b, o->mat);
 	return o;
 }
diff --git a/main.c b/main.c
index 1a18559..b103798 100644
--- a/main.c
+++ b/main.c
@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.10-r915-dirty"
+#define PACKAGE_VERSION "0.7.10-r926-dirty"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);