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Name: bfast
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Version: 0.7.0a
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Release: 31%{?dist}
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Summary: Blat-like Fast Accurate Search Tool
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License: GPLv2 and MIT
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URL: https://github.com/nh13/BFAST
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Source0: http://downloads.sourceforge.net/%{name}/%{name}-%{version}.tar.gz
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Patch0: %{name}-pthread-new.patch
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BuildRequires: autoconf
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BuildRequires: automake
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BuildRequires: gcc
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BuildRequires: perl-generators
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BuildRequires: zlib-devel
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BuildRequires: bzip2-devel
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BuildRequires: make
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%description
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BFAST facilitates the fast and accurate mapping of short reads to
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reference sequences. Some advantages of BFAST include:
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Speed: enables billions of short reads to be mapped quickly.
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Accuracy: A priori probabilities for mapping reads with defined set of variants.
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An easy way to measurably tune accuracy at the expense of speed.
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Specifically, BFAST was designed to facilitate whole-genome
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resequencing, where mapping billions of short reads with variants is
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of utmost importance.
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BFAST supports both Illumina and ABI SOLiD data, as well as any other
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Next-Generation Sequencing Technology (454, Helicos), with particular
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emphasis on sensitivity towards errors, SNPs and especially
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indels. Other algorithms take short-cuts by ignoring errors, certain
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types of variants (indels), and even require further alignment, all to
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be the "fastest" (but still not complete). BFAST is able to be tuned
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to find variants regardless of the error-rate, polymorphism rate, or
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other factors.
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%prep
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%setup -q
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%patch0 -p1
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# Let configure honor CFLAGS
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sed -i -e 's,^\(CFLAGS="${default_CFLAGS} ${extended_CFLAGS}"\),# \1,' configure.ac
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# Regenerate butil/Makefile.in to retain
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# balignmentscoredistribution_LDADD=-lpthread, otherwise the build fails with
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# --as-needed in LDFLAGS, bug #1674691
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autoreconf -fi
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%build
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# Package expects gnu89 inline semantics
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%configure "CFLAGS=${CFLAGS} -fgnu89-inline"
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%make_build
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%install
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%make_install
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rm %{buildroot}/%{_docdir}/%{name}/LICENSE
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rm %{buildroot}/%{_docdir}/%{name}/bfast-book.pdf
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%files
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%doc AUTHORS ChangeLog NEWS README
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%doc manual/bfast-book.pdf
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%license LICENSE
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%{_bindir}/balignmentscoredistribution
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%{_bindir}/balignsim
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%{_bindir}/bevalsim
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%{_bindir}/bfast
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%{_bindir}/bfast.resubmit.pl
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%{_bindir}/bfast.submit.pl
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%{_bindir}/bgeneratereads
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%{_bindir}/bindexdist
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%{_bindir}/bindexhist
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%{_bindir}/bmfmerge
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%{_bindir}/brepeat
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%{_bindir}/btestindexes
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%{_bindir}/ill2fastq.pl
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%{_bindir}/solid2fastq
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%changelog
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* Wed Jan 18 2023 Fedora Release Engineering <releng@fedoraproject.org> - 0.7.0a-31
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild
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8c364af |
* Wed Jul 20 2022 Fedora Release Engineering <releng@fedoraproject.org> - 0.7.0a-30
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild
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8c364af |
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aeb5571 |
* Wed Jan 19 2022 Fedora Release Engineering <releng@fedoraproject.org> - 0.7.0a-29
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild
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aeb5571 |
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a948942 |
* Wed Jul 21 2021 Fedora Release Engineering <releng@fedoraproject.org> - 0.7.0a-28
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild
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f18b017 |
* Tue Jan 26 2021 Fedora Release Engineering <releng@fedoraproject.org> - 0.7.0a-27
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild
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f18b017 |
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* Fri Jan 01 2021 Filipe Rosset <rosset.filipe@gmail.com> - 0.7.0a-26
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- Fix FTBFS rhbz#1863246
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* Sat Aug 01 2020 Fedora Release Engineering <releng@fedoraproject.org> - 0.7.0a-25
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- Second attempt - Rebuilt for
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https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild
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* Mon Jul 27 2020 Fedora Release Engineering <releng@fedoraproject.org> - 0.7.0a-24
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild
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* Tue Jan 28 2020 Fedora Release Engineering <releng@fedoraproject.org> - 0.7.0a-23
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild
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* Wed Jul 24 2019 Fedora Release Engineering <releng@fedoraproject.org> - 0.7.0a-22
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild
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* Mon Jul 15 2019 Petr Pisar <ppisar@redhat.com> - 0.7.0a-21
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- Regenerate a build script (bug #1674691)
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- Upstream moved to <https://github.com/nh13/BFAST>
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* Thu Jan 31 2019 Fedora Release Engineering <releng@fedoraproject.org> - 0.7.0a-20
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild
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* Thu Jul 12 2018 Fedora Release Engineering <releng@fedoraproject.org> - 0.7.0a-19
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild
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* Wed Feb 07 2018 Fedora Release Engineering <releng@fedoraproject.org> - 0.7.0a-18
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9bb3835 |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild
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* Wed Aug 02 2017 Fedora Release Engineering <releng@fedoraproject.org> - 0.7.0a-17
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild
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* Wed Jul 26 2017 Fedora Release Engineering <releng@fedoraproject.org> - 0.7.0a-16
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild
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* Fri Feb 10 2017 Fedora Release Engineering <releng@fedoraproject.org> - 0.7.0a-15
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild
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* Fri Feb 19 2016 Ralf Cors├ępius <corsepiu@fedoraproject.org> - 0.7.0a-14
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- Let configure honor CFLAGS (F24FTBFS, RHBZ#1307345).
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- Append -fgnu89-inline to CFLAGS.
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- Re-enable hardening.
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- Add %%license.
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- Modernize spec.
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* Wed Feb 03 2016 Fedora Release Engineering <releng@fedoraproject.org> - 0.7.0a-13
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild
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* Sun Jul 05 2015 Adam Huffman <bloch@verdurin.com> - 0.7.0a-12
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- Disable hardened build temporarily to work around configure problem
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* Wed Jun 17 2015 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.7.0a-11
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild
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* Fri Aug 15 2014 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.7.0a-10
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild
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* Sat Jun 07 2014 Adam Huffman <bloch@verdurin.com> - 0.7.0a-9
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- More aarch64 build fixes
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- Update pthread patch
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* Sat Jun 07 2014 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.7.0a-8
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild
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* Mon Jun 02 2014 Adam Huffman <bloch@verdurin.com> - 0.7.0a-7
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19e6567 |
- Fix for building on aarch64
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19e6567 |
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0903d37 |
* Sat Aug 03 2013 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.7.0a-6
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0903d37 |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild
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0903d37 |
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d5f124b |
* Wed Jul 17 2013 Petr Pisar <ppisar@redhat.com> - 0.7.0a-5
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- Perl 5.18 rebuild
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7ad29d9 |
* Wed Feb 13 2013 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.7.0a-4
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7ad29d9 |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild
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7ad29d9 |
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dfc4785 |
* Wed Jul 18 2012 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.7.0a-3
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dfc4785 |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild
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dfc4785 |
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48561a1 |
* Thu Jan 12 2012 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.7.0a-2
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48561a1 |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_17_Mass_Rebuild
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48561a1 |
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* Tue Nov 1 2011 Adam Huffman <bloch@verdurin.com> - 0.7.0a-1
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- new upstream release 0.7.0a including paired end and mate pair improvements
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* Fri May 27 2011 Adam Huffman <bloch@verdurin.com> - 0.6.5a-1
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- new upstream release
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- remove obsolete file deletion
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* Mon Feb 07 2011 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.6.4e-2
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7edc7df |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_15_Mass_Rebuild
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* Thu Oct 14 2010 Adam Huffman <bloch@verdurin.com> - 0.6.4e-1
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- new upstream bugfix release
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- solid2fastq.pl removed upstream
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* Wed Jun 23 2010 Adam Huffman <bloch@verdurin.com> - 0.6.4d-5
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- add MIT licence for kseq.h
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- improve description
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- clean up URL
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* Tue Jun 22 2010 Adam Huffman <bloch@verdurin.com> - 0.6.4d-4
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- add temporary fix for problem with 32-bit build
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* Wed Jun 16 2010 Adam Huffman <bloch@verdurin.com> - 0.6.4d-3
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- temporary release with solid2fastq.pl removed, to avoid conflict with bwa
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* Mon Jun 7 2010 Adam Huffman <bloch@verdurin.com> - 0.6.4d-2
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- add BR for zlib and bz2
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- patch to add pthread to linking stage
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- remove two docs installed by upstream Makefile, to avoid clash with docs
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* Thu Jun 3 2010 Adam Huffman <bloch@verdurin.com> - 0.6.4d-1
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- initial version
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