From 3efb7c0e91e5232f4858d9e6033bd5eb9de2348b Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Mon, 31 Mar 2014 15:27:23 -0400
Subject: [PATCH] r455: release bwa-0.7.8

---
 NEWS      | 32 ++++++++++++++++++++++++++++++++
 bwa.1     |  7 +++++++
 fastmap.c |  4 ++--
 main.c    |  2 +-
 4 files changed, 42 insertions(+), 3 deletions(-)

diff --git a/NEWS b/NEWS
index a7c64ed..40f4433 100644
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,35 @@
+Release 0.7.8 (31 March, 2014)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Changes in BWA-MEM:
+
+ * Bugfix: off-diagonal X-dropoff (option -d) not working as intended.
+   Short-read alignment is not affected.
+
+ * Bugfix: unnecessarily large bandwidth used during global alignment,
+   which reduces the mapping speed by ~5% for short reads. Results are not
+   affected.
+
+ * Bugfix: when the matching score is not one, paired-end mapping quality is
+   inaccurate.
+
+ * When the matching score (option -A) is changed, scale all score-related
+   options accordingly unless overridden by users.
+
+ * Allow to specify different gap open (or extension) penalties for deletions
+   and insertions separately.
+
+ * Allow to specify the insert size distribution.
+
+ * Better and more detailed debugging information.
+
+With the default setting, 0.7.8 and 0.7.7 gave identical output on one million
+100bp read pairs.
+
+(0.7.8: 31 March 2014, r455)
+
+
+
 Release 0.7.7 (25 Feburary, 2014)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
diff --git a/bwa.1 b/bwa.1
index 47bdd61..b6354e5 100644
--- a/bwa.1
+++ b/bwa.1
@@ -267,6 +267,13 @@ supported throughout BWA. Ideally, a value 0 for disabling all the output to
 stderr; 1 for outputting errors only; 2 for warnings and errors; 3 for
 all normal messages; 4 or higher for debugging. When this option takes value
 4, the output is not SAM. [3]
+.TP
+.BI -I \ FLOAT[,FLOAT[,INT[,INT]]]
+Specify the mean, standard deviation (10% of the mean if absent), max (4 sigma
+from the mean if absent) and min (4 sigma if absent) of the insert size
+distribution. Only applicable to the FR orientation. By default, BWA-MEM infers
+these numbers and the pair orientations given enough reads. [inferred]
+
 .RE
 
 .TP
diff --git a/fastmap.c b/fastmap.c
index 5d6d9d6..093fb7b 100644
--- a/fastmap.c
+++ b/fastmap.c
@@ -132,8 +132,8 @@ int main_mem(int argc, char *argv[])
 		fprintf(stderr, "       -C            append FASTA/FASTQ comment to SAM output\n");
 		fprintf(stderr, "       -M            mark shorter split hits as secondary\n\n");
 		fprintf(stderr, "       -I FLOAT[,FLOAT[,INT[,INT]]]\n");
-		fprintf(stderr, "                     specify the mean, standard deviation (10%% of mean if absent), max (4\n");
-		fprintf(stderr, "                     sigma from the mean if absent) and min of the insert size distribution.\n");
+		fprintf(stderr, "                     specify the mean, standard deviation (10%% of the mean if absent), max\n");
+		fprintf(stderr, "                     (4 sigma from the mean if absent) and min of the insert size distribution.\n");
 		fprintf(stderr, "                     FR orientation only. [inferred]\n");
 		fprintf(stderr, "\nNote: Please read the man page for detailed description of the command line and options.\n");
 		fprintf(stderr, "\n");
diff --git a/main.c b/main.c
index 5a983c9..0ae7978 100644
--- a/main.c
+++ b/main.c
@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.7+dev-r454"
+#define PACKAGE_VERSION "0.7.8-r455"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);