debian/changelog

+qtltools (1.2+dfsg-1) UNRELEASED; urgency=medium
+
+  * New upstream release.
+  * Update d/copyright.
+  * Bump Standards-Version to 4.4.1 (no changes needed).
+  * Bump debhelper compat 12.
+
+ -- Dylan Aïssi <daissi@debian.org>  Mon, 30 Sep 2019 22:04:06 +0200
+
 qtltools (1.1+dfsg-3) unstable; urgency=medium
 
   * Team upload.
@@ -31,7 +40,7 @@ qtltools (1.1+dfsg-2) unstable; urgency=medium
 qtltools (1.1+dfsg-1) unstable; urgency=medium
 
   * Team upload.
-  * New upstram version
+  * New upstream version
   * d/watch: version=4
 
  -- Andreas Tille <tille@debian.org>  Mon, 16 Jan 2017 10:06:15 +0100

debian/compat

-11
+12

debian/control

 Source: qtltools
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
-Uploaders: Dylan Aïssi <bob.dybian@gmail.com>
+Uploaders: Dylan Aïssi <daissi@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper (>= 12~),
                libblas-dev,
                libboost-iostreams-dev,
                libboost-program-options-dev,
@@ -13,7 +13,7 @@ Build-Depends: debhelper (>= 11~),
                libhts-dev,
                r-mathlib,
                zlib1g-dev
-Standards-Version: 4.2.1
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/qtltools
 Vcs-Git: https://salsa.debian.org/med-team/qtltools.git
 Homepage: https://qtltools.github.io/qtltools/

debian/copyright

@@ -8,11 +8,15 @@ Files-Excluded: bin
                 obj
 
 Files: *
-Copyright: 2016 Olivier Delaneau, Halit Ongen and Emmanouil T. Dermitzakis
+Copyright: 2016-2019 Olivier Delaneau, Halit Ongen and Emmanouil T. Dermitzakis
 License: GPL-3+
 
+Files: src/mode_quan/quan_xxhash.cpp
+Copyright: 2012-2016 Yann Collet (xxHash project - https://github.com/Cyan4973/xxHash)
+License: BSD-2-clause
+
 Files: debian/*
-Copyright: 2016 Dylan Aïssi <bob.dybian@gmail.com>
+Copyright: 2016-2019 Dylan Aïssi <daissi@debian.org>
 License: GPL-3+
 
 License: GPL-3+
@@ -32,3 +36,28 @@ License: GPL-3+
  .
  On Debian systems, the full text of the GNU General Public License
  version 3 can be found in `/usr/share/common-licenses/GPL-3'.
+
+License: BSD-2-clause
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are
+ met:
+ .
+   1. Redistributions of source code must retain the above copyright
+      notice, this list of conditions and the following disclaimer.
+ .
+   2. Redistributions in binary form must reproduce the above copyright
+      notice, this list of conditions and the following disclaimer listed
+      in this license in the documentation and/or other materials
+      provided with the distribution.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+ A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+ OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+ THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

debian/patches/Makefile_config.patch

 Author: Dylan Aïssi
 Description: Configure the makefile for Debian packaging.
-Last-Update: 2016-11-02
+Last-Update: 2019-09-30
 Forwarded: not-needed
 
 --- a/Makefile
 +++ b/Makefile
-@@ -28,7 +28,7 @@ OFILE=$(shell for file in `find src -nam
+@@ -28,11 +28,7 @@
  VPATH=$(shell for file in `find src -name *.cpp`; do echo $$(dirname $$file); done)
  
- #DEFAULT VERSION (I.E. UNIGE DESKTOP RELEASE VERSION)
--all: desktop
+ #DEFAULT VERSION (SET UP THE VARIABLES IN THE BEGINING OF THE MAKEFILE)
+-all: CXXFLAG=$(CXXFLAG_REL) $(CXXFLAG_WRN)
+-all: IFLAG=-Ilib/OTools -Ilib -I$(RMATH_INC) -I$(HTSLD_INC) -I$(BOOST_INC)
+-all: LIB_FILES=$(RMATH_LIB)/libRmath.a $(HTSLD_LIB)/libhts.a $(BOOST_LIB)/libboost_iostreams.a $(BOOST_LIB)/libboost_program_options.a
+-all: LDFLAG=$(CXXFLAG_REL)
+-all: $(BFILE)
 +all: debian
  
- #UNIGE DESKTOP RELEASE VERSION
- desktop: RMATH_INC=$(HOME)/Tools/R-3.2.2/src/include
-@@ -92,6 +92,14 @@ mac-dbg: LIB_FILES=$(RMATH_LIB)/libRmath
+ #DEFAULT DEBUG VERSION (SET UP THE VARIABLES IN THE BEGINING OF THE MAKEFILE)
+ all-dbg: CXXFLAG=$(CXXFLAG_DBG) $(CXXFLAG_WRN)
+@@ -129,6 +125,14 @@
  mac-dbg: LDFLAG=$(CXXFLAG_DBG) -L /opt/local/lib
  mac-dbg: $(BFILE)
  

debian/patches/Spelling_error.patch

 Author: Dylan Aïssi
 Description: Fix spelling error.
-Last-Update: 2016-11-16
+Last-Update: 2019-09-30
 Forwarded: https://github.com/qtltools/qtltools/pull/3
 
 --- a/src/mode_fdensity/fdensity_main.cpp
 +++ b/src/mode_fdensity/fdensity_main.cpp
-@@ -30,7 +30,7 @@
- 
- 	boost::program_options::options_description opt_parameters ("\x1B[32mParameters\33[0m");
- 	opt_parameters.add_options()
--		("window", boost::program_options::value< int >()->default_value(1000000), "Window size arround TSS in bp.")
-+		("window", boost::program_options::value< int >()->default_value(1000000), "Window size around TSS in bp.")
- 		("bin", boost::program_options::value< int >()->default_value(1000), "Bin size in bp.");
- 
- 	D.option_descriptions.add(opt_files).add(opt_parameters);
 @@ -49,7 +49,7 @@
  	//---------------------
  	// 3. PRINT HELP/HEADER

debian/patches/reproducible_build.patch

@@ -5,7 +5,7 @@ Forwarded: TODO
 
 --- a/Makefile
 +++ b/Makefile
-@@ -23,8 +23,8 @@ LIB_FLAGS=-Wl,-Bstatic -lz -lgsl -lblas
+@@ -23,8 +23,8 @@
  BFILE=bin/QTLtools
  HFILE=$(shell find src -name *.h)
  TFILE=$(shell find lib -name *.h)
@@ -15,4 +15,4 @@ Forwarded: TODO
 +OFILE=$(shell for file in `find src -name *.cpp | LC_ALL=C sort`; do echo obj/$$(basename $$file .cpp).o; done)
  VPATH=$(shell for file in `find src -name *.cpp`; do echo $$(dirname $$file); done)
  
- #DEFAULT VERSION (I.E. UNIGE DESKTOP RELEASE VERSION)
+ #DEFAULT VERSION (SET UP THE VARIABLES IN THE BEGINING OF THE MAKEFILE)

debian/rules

@@ -18,4 +18,3 @@ override_dh_auto_clean:
 override_dh_install:
 	cd debian/upstream.example && find -type f | LC_ALL=C sort | tar -T - --sort=name --mode=go=rX,u+rw,a-s --owner=root --group=root --numeric-owner -Jcvf examples.tar.xz
 	dh_install
-