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Name: bfast
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720230e |
Version: 0.7.0a
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dfc4785 |
Release: 3%{?dist}
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Summary: Blat-like Fast Accurate Search Tool
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Group: Applications/Engineering
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License: GPLv2 and MIT
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URL: http://bfast.sourceforge.net
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Source0: http://downloads.sourceforge.net/%{name}/%{name}-%{version}.tar.gz
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Patch0: %{name}-pthread.patch
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BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
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BuildRequires: zlib-devel bzip2-devel
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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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# temporary fix for 32-bit build problem
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sed -i '/^extended_CFLAGS=/ s/-m64//' configure
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%build
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%configure
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make %{?_smp_mflags} CFLAGS="%{optflags}"
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%install
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rm -rf %{buildroot}
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make install DESTDIR=%{buildroot}
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rm %{buildroot}/%{_docdir}/%{name}/LICENSE
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rm %{buildroot}/%{_docdir}/%{name}/bfast-book.pdf
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%clean
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rm -rf %{buildroot}
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%files
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%defattr(-,root,root,-)
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%doc AUTHORS ChangeLog NEWS README LICENSE
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%doc manual/bfast-book.pdf
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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 Jul 18 2012 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.7.0a-3
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild
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* Thu Jan 12 2012 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.7.0a-2
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_17_Mass_Rebuild
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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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- 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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