debian/changelog

-diamond-aligner (0.9.25+dfsg-1) UNRELEASED; urgency=medium
+diamond-aligner (0.9.25+dfsg-1) unstable; urgency=medium
 
   * New upstream version
   * debhelper-compat 12
   * Standards-Version: 4.4.0
-  TODO: Build issue see
-        https://github.com/bbuchfink/diamond/issues/295
+  * Drop unneeded paragraph from d/copyright
 
- -- Andreas Tille <tille@debian.org>  Wed, 31 Jul 2019 14:57:15 +0200
+ -- Andreas Tille <tille@debian.org>  Thu, 01 Aug 2019 15:00:33 +0200
 
 diamond-aligner (0.9.24+dfsg-1) unstable; urgency=medium
 

debian/copyright

@@ -9,29 +9,6 @@ Files: *
 Copyright: 2014-2016, University of Tuebingen, Benjamin Buchfink
 License: BSD-3-clause
 
-Files: src/util/fast_mutex.h
-       src/util/tinythread.*
-Copyright: 2010-2012 Marcus Geelnard
-License: as-is
- This software is provided 'as-is', without any express or implied
- warranty. In no event will the authors be held liable for any damages
- arising from the use of this software.
- .
- Permission is granted to anyone to use this software for any purpose,
- including commercial applications, and to alter it and redistribute it
- freely, subject to the following restrictions:
- .
-    1. The origin of this software must not be misrepresented; you must not
-    claim that you wrote the original software. If you use this software
-    in a product, an acknowledgment in the product documentation would be
-    appreciated but is not required.
- .
-    2. Altered source versions must be plainly marked as such, and must not be
-    misrepresented as being the original software.
- .
-    3. This notice may not be removed or altered from any source
-    distribution.
-
 Files: debian/*
 Copyright: 2016 Andreas Tille <tille@debian.org>
 License: BSD-3-clause

debian/patches/82feea2aee5c82e283704b9317cb5e8abc625f90.patch

+From 82feea2aee5c82e283704b9317cb5e8abc625f90 Mon Sep 17 00:00:00 2001
+From: Benjamin Buchfink <buchfink@gmail.com>
+Date: Thu, 1 Aug 2019 14:36:14 +0200
+Subject: [PATCH] Fixed #295.
+
+---
+ src/dp/needleman_wunsch.cpp | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/dp/needleman_wunsch.cpp b/src/dp/needleman_wunsch.cpp
+index abb47bb..2050eea 100644
+--- a/src/dp/needleman_wunsch.cpp
++++ b/src/dp/needleman_wunsch.cpp
+@@ -167,7 +167,7 @@ const Fixed_score_buffer<_score>& needleman_wunsch(sequence query, sequence subj
+ 	return mtx.score_buffer();
+ }
+ 
+-template const Fixed_score_buffer<int>& needleman_wunsch(sequence query, sequence subject, int &max_score, const Local&, const int&);
++// template const Fixed_score_buffer<int>& needleman_wunsch(sequence query, sequence subject, int &max_score, const Local&, const int&);
+ 
+ int needleman_wunsch(sequence query, sequence subject, int qbegin, int qend, int sbegin, int send, unsigned node, unsigned edge, Diag_graph &diags, bool log)
+ {

debian/patches/series

 avoid_unwanted_optimisation.patch
 no_march_native.patch
+82feea2aee5c82e283704b9317cb5e8abc625f90.patch