Rebuilt for https://fedoraproject.org/wiki/Fedora_45_Mass_Rebuild

This is part of https://fedoraproject.org/wiki/Changes/SPDX_Licenses_Phase_4

.gitignore

@@ -1 +1,6 @@
 /vcftools_0.1.9.tar.gz
+/vcftools_0.1.11.tar.gz
+/vcftools-0.1.14.tar.gz
+/vcftools-0.1.15.tar.gz
+/vcftools-0.1.16.tar.gz
+/vcftools-0.1.17.tar.gz

changelog

@@ -0,0 +1,156 @@
+* Fri Jul 25 2025 Fedora Release Engineering <releng@fedoraproject.org> - 0.1.16-22
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_43_Mass_Rebuild
+
+* Sun Jan 19 2025 Fedora Release Engineering <releng@fedoraproject.org> - 0.1.16-21
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_42_Mass_Rebuild
+
+* Mon Jul 29 2024 Miroslav Suchý <msuchy@redhat.com> - 0.1.16-20
+- convert license to SPDX
+
+* Sat Jul 20 2024 Fedora Release Engineering <releng@fedoraproject.org> - 0.1.16-19
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_41_Mass_Rebuild
+
+* Sat Jan 27 2024 Fedora Release Engineering <releng@fedoraproject.org> - 0.1.16-18
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild
+
+* Sat Jul 22 2023 Fedora Release Engineering <releng@fedoraproject.org> - 0.1.16-17
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild
+
+* Sat Jan 21 2023 Fedora Release Engineering <releng@fedoraproject.org> - 0.1.16-16
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild
+
+* Thu Sep 01 2022 Filipe Rosset <rosset.filipe@gmail.com> - 0.1.16-15
+- spec cleanup and modernization
+
+* Sat Jul 23 2022 Fedora Release Engineering <releng@fedoraproject.org> - 0.1.16-14
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild
+
+* Mon May 30 2022 Jitka Plesnikova <jplesnik@redhat.com> - 0.1.16-13
+- Perl 5.36 rebuild
+
+* Sat Jan 22 2022 Fedora Release Engineering <releng@fedoraproject.org> - 0.1.16-12
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild
+
+* Fri Jul 23 2021 Fedora Release Engineering <releng@fedoraproject.org> - 0.1.16-11
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild
+
+* Fri May 21 2021 Jitka Plesnikova <jplesnik@redhat.com> - 0.1.16-10
+- Perl 5.34 rebuild
+
+* Wed Jan 27 2021 Fedora Release Engineering <releng@fedoraproject.org> - 0.1.16-9
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild
+
+* Wed Jul 29 2020 Fedora Release Engineering <releng@fedoraproject.org> - 0.1.16-8
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild
+
+* Fri Jun 26 2020 Jitka Plesnikova <jplesnik@redhat.com> - 0.1.16-7
+- Perl 5.32 re-rebuild of bootstrapped packages
+
+* Mon Jun 22 2020 Jitka Plesnikova <jplesnik@redhat.com> - 0.1.16-6
+- Perl 5.32 rebuild
+
+* Fri Jan 31 2020 Fedora Release Engineering <releng@fedoraproject.org> - 0.1.16-5
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild
+
+* Sat Jul 27 2019 Fedora Release Engineering <releng@fedoraproject.org> - 0.1.16-4
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild
+
+* Mon Jun 17 2019 Petr Pisar <ppisar@redhat.com> - 0.1.16-3
+- Install Perl modules into a vendor Perl path
+
+* Sun Feb 03 2019 Fedora Release Engineering <releng@fedoraproject.org> - 0.1.16-2
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild
+
+* Sun Aug 05 2018 Adam Huffman <bloch@verdurin.com> - 0.1.16-1
+- Update to latest upstream release 0.1.16
+
+* Sat Jul 14 2018 Fedora Release Engineering <releng@fedoraproject.org> - 0.1.15-7
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild
+
+* Mon Apr 09 2018 Filipe Rosset <rosset.filipe@gmail.com> - 0.1.15-6
+- added gcc-c++ as BR
+
+* Fri Feb 09 2018 Fedora Release Engineering <releng@fedoraproject.org> - 0.1.15-5
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild
+
+* Thu Aug 03 2017 Fedora Release Engineering <releng@fedoraproject.org> - 0.1.15-4
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild
+
+* Thu Jul 27 2017 Fedora Release Engineering <releng@fedoraproject.org> - 0.1.15-3
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild
+
+* Mon May 15 2017 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.1.15-2
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_26_27_Mass_Rebuild
+
+* Fri Apr 21 2017 Filipe Rosset <rosset.filipe@gmail.com> - 0.1.15-1
+- Update to latest upstream release 0.1.15
+
+* Sat Feb 11 2017 Fedora Release Engineering <releng@fedoraproject.org> - 0.1.14-2
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild
+
+* Tue Nov 08 2016 Filipe Rosset <rosset.filipe@gmail.com> - 0.1.14-1
+- Update to latest upstream release 0.1.14
+- Fix FTBFS rhbz #1308219
+- Fix rhbz #1365319 thanks to Aram Minasyan
+- Spec modernization/clean up, new URLs from GitHub
+
+* Fri Feb 05 2016 Fedora Release Engineering <releng@fedoraproject.org> - 0.1.11-9
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild
+
+* Fri Jun 19 2015 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.1.11-8
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild
+
+* Sat May 02 2015 Kalev Lember <kalevlember@gmail.com> - 0.1.11-7
+- Rebuilt for GCC 5 C++11 ABI change
+
+* Mon Aug 18 2014 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.1.11-6
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild
+
+* Sun Jun 08 2014 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.1.11-5
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild
+
+* Sat Aug 03 2013 Petr Pisar <ppisar@redhat.com> - 0.1.11-4
+- Perl 5.18 rebuild
+
+* Tue Jul 30 2013 Peter Robinson <pbrobinson@fedoraproject.org> 0.1.11-3
+- Use distro CFLAGS (fix FTBFS on ARM)
+
+* Thu Jul 18 2013 Petr Pisar <ppisar@redhat.com> - 0.1.11-2
+- Perl 5.18 rebuild
+
+* Wed Jul 03 2013 <bloch@verdurin.com> - 0.1.11-1
+- Update to latest upstream release 0.1.11
+
+* Fri Feb 15 2013 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.1.9-2
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild
+
+* Sun Jul 29 2012  <bloch@verdurin.com> - 0.1.9-1
+- Update to 0.1.9
+- Remove perl patch that's no longer needed
+
+* Thu Jan  5 2012 Adam Huffman <verdurin@fedoraproject.org> - 0.1.7-1
+- update to upstream release 0.1.7
+- remove fill-rsIDs
+- update Perl makefile patch
+
+* Sun Jul 31 2011 Adam Huffman <bloch@verdurin.com> - 0.1.6-1
+- update to 0.1.6
+
+* Tue May  3 2011 Adam Huffman <bloch@verdurin.com> - 0.1.5-2
+- minor fix to Jack's Perl patch
+- permissions fix
+- hardcoded path fix
+- cleaner Makefile fix
+
+* Sun May 1 2011 Jack Tanner <ihok@hotmail.com> - 0.1.5-1
+- bump to 0.1.5
+- rename compare-vcf, merge-vcf, and query-vcf to vcf-compare,
+  vcf-merge, and vcf-query
+- add VcfStats.pm to perl export
+- patch perl/Makefile to export VcfStats.pm
+
+* Mon Mar 21 2011 Adam Huffman <bloch@verdurin.com> - 0.1.4a-1
+- initial version
+- fix CPPFLAGS
+- fix hardcoded installation location
+

sources

@@ -1 +1 @@
-57f3b8d7ecb26a12559595851607f023  vcftools_0.1.9.tar.gz
+SHA512 (vcftools-0.1.17.tar.gz) = 8adf2490b5d0886302f8f19efc735e4b96d657d70a764b6fa397acdf6f83b54da29dc73e9b96b275a793a511996c415630255610249e6eb5441bc783e82853d9

vcftools.spec

@@ -1,18 +1,17 @@
 Name:		vcftools
-Version:	0.1.9
-Release:	1%{?dist}
+Version:	0.1.17
+Release:	%autorelease
 Summary:	VCF file manipulation tools
-
-Group:		Applications/Engineering
-License:	GPLv3 
-URL:		http://vcftools.sourceforge.net/
-Source0:	http://downloads.sourceforge.net/%{name}/%{name}_%{version}.tar.gz
-
-BuildRoot:	%{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
-
+# Automatically converted from old format: GPLv3 - review is highly recommended.
+License:	GPL-3.0-only 
+URL:		https://vcftools.github.io/
+Source0:	https://github.com/%{name}/%{name}/releases/download/v%{version}/%{name}-%{version}.tar.gz
+BuildRequires:	make
+BuildRequires:	gcc-c++
+BuildRequires:	perl-generators
+BuildRequires:	perl-interpreter
 BuildRequires:	zlib-devel
 
-
 %description
 A program package designed for working with VCF files, such as those
 generated by the 1000 Genomes Project. The aim of VCFtools is to
@@ -20,28 +19,23 @@ provide methods for working with VCF files: validating, merging,
 comparing and calculate some basic population genetic statistics.
 
 %prep
-%setup -q -n %{name}_%{version}
-#%patch0 -p1
+%autosetup
 
 %build
-make %{?_smp_mflags} CPPFLAGS="%{optflags}"
+%configure --with-pmdir=%(perl -e 'print $ARGV[0] =~ s{\A\Q$ARGV[1]\E/}{}r' \
+    %{perl_vendorlib} %{_exec_prefix})
+%make_build
 
+%check
+make check
 
 %install
-rm -rf %{buildroot}
-make install PREFIX=%{buildroot}/usr MODDIR="%{buildroot}/%{perl_vendorarch}" \
-BINDIR="%{buildroot}/%{_bindir}"
-
-install -m 0775 %{_builddir}/%{name}_%{version}/cpp/vcftools %{buildroot}/%{_bindir}
-
-
-%clean
-rm -rf %{buildroot}
+%make_install
 
 
 %files
-%defattr(-,root,root,-)
-%doc README.txt
+%doc README.md
+%license LICENSE
 %{_bindir}/vcf-compare
 %{_bindir}/fill-aa
 %{_bindir}/fill-an-ac
@@ -57,39 +51,21 @@ rm -rf %{buildroot}
 %{_bindir}/vcf-subset
 %{_bindir}/vcf-to-tab
 %{_bindir}/vcf-validator
-%attr(0755, root, root) %{_bindir}/vcftools
-%{perl_vendorarch}/FaSlice.pm
-%{perl_vendorarch}/Vcf.pm
-%{perl_vendorarch}/VcfStats.pm
+%{_bindir}/fill-fs
+%{_bindir}/fill-ref-md5
+%{_bindir}/vcf-consensus
+%{_bindir}/vcf-contrast
+%{_bindir}/vcf-fix-ploidy
+%{_bindir}/vcf-indel-stats
+%{_bindir}/vcf-phased-join
+%{_bindir}/vcf-shuffle-cols
+%{_bindir}/vcf-tstv
+%{_bindir}/vcf-fix-newlines
+%{_bindir}/vcftools
+%{perl_vendorlib}/FaSlice.pm
+%{perl_vendorlib}/Vcf.pm
+%{perl_vendorlib}/VcfStats.pm
+%{_mandir}/man1/vcftools.1.gz
 
 %changelog
-* Sun Jul 29 2012  <bloch@verdurin.com> - 0.1.9-1
-- Update to 0.1.9
-- Remove perl patch that's no longer needed
-
-* Thu Jan  5 2012 Adam Huffman <verdurin@fedoraproject.org> - 0.1.7-1
-- update to upstream release 0.1.7
-- remove fill-rsIDs
-- update Perl makefile patch
-
-* Sun Jul 31 2011 Adam Huffman <bloch@verdurin.com> - 0.1.6-1
-- update to 0.1.6
-
-* Tue May  3 2011 Adam Huffman <bloch@verdurin.com> - 0.1.5-2
-- minor fix to Jack's Perl patch
-- permissions fix
-- hardcoded path fix
-- cleaner Makefile fix
-
-* Sun May 1 2011 Jack Tanner <ihok@hotmail.com> - 0.1.5-1
-- bump to 0.1.5
-- rename compare-vcf, merge-vcf, and query-vcf to vcf-compare,
-  vcf-merge, and vcf-query
-- add VcfStats.pm to perl export
-- patch perl/Makefile to export VcfStats.pm
-
-* Mon Mar 21 2011 Adam Huffman <bloch@verdurin.com> - 0.1.4a-1
-- initial version
-- fix CPPFLAGS
-- fix hardcoded installation location
-
+%autochangelog