Add patch to ensure compatibility with C++11 iostream
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12
mmseq-iostream-c++11.patch
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12
mmseq-iostream-c++11.patch
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@ -0,0 +1,12 @@
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diff -ur mmseq-1.0.8a/src/hitsio.cpp mmseq-1.0.8a.new/src/hitsio.cpp
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--- mmseq-1.0.8a/src/hitsio.cpp 2014-01-09 22:45:54.000000000 +0000
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+++ mmseq-1.0.8a.new/src/hitsio.cpp 2016-02-12 09:46:01.800529284 +0000
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@@ -343,7 +343,7 @@
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bool HitsfileReader::readReadMapRecordTranscriptIDSchema0(string &transcriptID) {
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if ((ifs.eof()) || (ifs.peek() == '>')) { return false; }
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- return(getline(ifs, transcriptID));
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+ return(static_cast<bool>(getline(ifs, transcriptID)));
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}
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void HitsfileReader::readHeaderSchema1(vector<string> *transcriptName, map<string, double> *transcriptEffectiveLength,
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@ -1,6 +1,6 @@
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Name: mmseq
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Name: mmseq
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Version: 1.0.8a
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Version: 1.0.8a
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Release: 9%{?dist}
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Release: 10%{?dist}
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Summary: Haplotype and isoform specific expression estimation for RNA-seq
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Summary: Haplotype and isoform specific expression estimation for RNA-seq
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Group: Applications/Engineering
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Group: Applications/Engineering
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@ -10,6 +10,7 @@ Source0: https://github.com/eturro/%{name}/archive/%{version}.zip
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Patch0: mmseq-sam-header.patch
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Patch0: mmseq-sam-header.patch
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#Patch1: mmseq-flags.patch
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#Patch1: mmseq-flags.patch
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Patch2: mmseq-zlib.patch
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Patch2: mmseq-zlib.patch
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Patch3: mmseq-iostream-c++11.patch
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BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
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BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
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BuildRequires: boost-devel
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BuildRequires: boost-devel
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@ -34,6 +35,8 @@ estimation using multi-mapping RNA-seq reads. Example scripts are included.
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#%%patch1 -p1 -b .mmseq-flags.patch
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#%%patch1 -p1 -b .mmseq-flags.patch
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#Fix zlib linking
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#Fix zlib linking
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%patch2 -p1 -b .mmseq-zlib.patch
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%patch2 -p1 -b .mmseq-zlib.patch
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#Fix for C++11 iostream changes
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%patch3 -p1 -b .mmseq-iostream-c++11.patch
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#Remove bundled binaries
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#Remove bundled binaries
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rm bin/*-linux
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rm bin/*-linux
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@ -86,6 +89,9 @@ rm -rf %{buildroot}
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%changelog
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%changelog
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* Fri Feb 12 2016 Adam Huffman <bloch@verdurin.com> - 1.0.8a-10
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- patch to add compatibility with C++11 iostream
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* Wed Feb 10 2016 Adam Huffman <bloch@verdurin.com> - 1.0.8a-9
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* Wed Feb 10 2016 Adam Huffman <bloch@verdurin.com> - 1.0.8a-9
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- rebuilt to pick up new armadillo
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- rebuilt to pick up new armadillo
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