[med-svn] [bwa] 03/03: Update to 0.7.16

[Steffen Möller]

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moeller pushed a commit to branch master
in repository bwa.

commit 58f6a77dcdadf6930f5e0150e23681971273a680
Author: Steffen Moeller <moeller at debian.org>
Date:   Mon Sep 11 15:51:25 2017 +0200

    Update to 0.7.16
---
 debian/changelog                          | 8 +++++---
 debian/control                            | 2 +-
 debian/patches/check_for_nan.patch        | 4 +++-
 debian/patches/fix_build_on_freebsd.patch | 8 +++++---
 debian/patches/series                     | 6 +++---
 debian/upstream/metadata                  | 1 -
 6 files changed, 17 insertions(+), 12 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index d60233f..28ca966 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,7 +1,9 @@
-bwa (0.7.15-6) UNRELEASED; urgency=medium
+bwa (0.7.16-1) unstable; urgency=medium
 
-  * debian/control: Policy bump tp 4.0.1
-  * debian/upstream/metadata: Add ref to OMICtools
+  * Team upload.
+
+  * debian/control: Policy bump tp 4.1.0
+  * debian/upstream/metadata: Add references to registries.
 
  -- Steffen Moeller <moeller at debian.org>  Mon, 07 Aug 2017 16:50:42 +0200
 
diff --git a/debian/control b/debian/control
index 8e3383d..726967c 100644
--- a/debian/control
+++ b/debian/control
@@ -9,7 +9,7 @@ Section: science
 Priority: optional
 Build-Depends: debhelper (>= 9),
                zlib1g-dev
-Standards-Version: 4.0.1
+Standards-Version: 4.1.0
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/bwa.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/bwa.git
 Homepage: http://bio-bwa.sourceforge.net/
diff --git a/debian/patches/check_for_nan.patch b/debian/patches/check_for_nan.patch
index 73fd9fa..a02175d 100644
--- a/debian/patches/check_for_nan.patch
+++ b/debian/patches/check_for_nan.patch
@@ -3,9 +3,11 @@ Description: check computed avg and std for nan
 Last-Update: 2017-07-03
 Bug: https://github.com/lh3/bwa/issues/108
 ===========================================================
+Index: bwa/bwtsw2_pair.c
+===================================================================
 --- bwa.orig/bwtsw2_pair.c
 +++ bwa/bwtsw2_pair.c
-@@ -85,6 +85,9 @@
+@@ -91,6 +91,9 @@ bsw2pestat_t bsw2_stat(int n, bwtsw2_t *
  	if (r.high < r.avg + MAX_STDDEV * r.std) r.high = (int)(r.avg + MAX_STDDEV * r.std + .499);
  	ksprintf(msg, "[%s] low and high boundaries for proper pairs: (%d, %d)\n", __func__, r.low, r.high);
  	free(isize);
diff --git a/debian/patches/fix_build_on_freebsd.patch b/debian/patches/fix_build_on_freebsd.patch
index 66885e0..cc2a678 100644
--- a/debian/patches/fix_build_on_freebsd.patch
+++ b/debian/patches/fix_build_on_freebsd.patch
@@ -2,9 +2,11 @@ Author: Andreas Tille <tille at debian.org>
 Last-Update: Fri, 10 Jul 2015 18:23:26 +0200
 Description: -lrt does not help only for Linux but also for freebsd
 
---- a/Makefile
-+++ b/Makefile
-@@ -17,6 +17,9 @@ SUBDIRS=	.
+Index: bwa/Makefile
+===================================================================
+--- bwa.orig/Makefile
++++ bwa/Makefile
+@@ -18,6 +18,9 @@ SUBDIRS=	.
  ifeq ($(shell uname -s),Linux)
  	LIBS += -lrt
  endif
diff --git a/debian/patches/series b/debian/patches/series
index 6687ece..52951e7 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,6 +1,6 @@
-print_unsigned_counts.patch
+#print_unsigned_counts.patch		# adopted upstream
 check_for_nan.patch
 fix_heap_block_overrun
 fix_build_on_freebsd.patch
-check_number_of_arguments.patch
-spelling.patch
+#check_number_of_arguments.patch	# adopted upstream
+#spelling.patch				# adopted upstream
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
index 59ea9a2..e024afc 100644
--- a/debian/upstream/metadata
+++ b/debian/upstream/metadata
@@ -27,4 +27,3 @@ Registry:
    Entry: BWA
  - Name: OMICtools
    Entry: OMICS_00654
- 

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