Add patch to ensure compatibility with C++11 iostream

mmseq-iostream-c++11.patch

@@ -0,0 +1,12 @@
+diff -ur mmseq-1.0.8a/src/hitsio.cpp mmseq-1.0.8a.new/src/hitsio.cpp
+--- mmseq-1.0.8a/src/hitsio.cpp	2014-01-09 22:45:54.000000000 +0000
++++ mmseq-1.0.8a.new/src/hitsio.cpp	2016-02-12 09:46:01.800529284 +0000
+@@ -343,7 +343,7 @@
+ 
+ bool HitsfileReader::readReadMapRecordTranscriptIDSchema0(string &transcriptID) {
+ 	if ((ifs.eof()) || (ifs.peek() == '>')) { return false; }
+-	return(getline(ifs, transcriptID));
++	return(static_cast<bool>(getline(ifs, transcriptID)));
+ }
+ 
+ void HitsfileReader::readHeaderSchema1(vector<string> *transcriptName, map<string, double> *transcriptEffectiveLength,

mmseq.spec

@@ -1,6 +1,6 @@
 Name:		mmseq
 Version:	1.0.8a
-Release:	9%{?dist}
+Release:	10%{?dist}
 Summary:	Haplotype and isoform specific expression estimation for RNA-seq
 
 Group:		Applications/Engineering
@@ -10,6 +10,7 @@ Source0:	https://github.com/eturro/%{name}/archive/%{version}.zip
 Patch0:		mmseq-sam-header.patch
 #Patch1:		mmseq-flags.patch
 Patch2:		mmseq-zlib.patch
+Patch3:		mmseq-iostream-c++11.patch
 BuildRoot:	%{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
 
 BuildRequires:	boost-devel
@@ -34,6 +35,8 @@ estimation using multi-mapping RNA-seq reads.  Example scripts are included.
 #%%patch1 -p1 -b .mmseq-flags.patch
 #Fix zlib linking
 %patch2 -p1 -b .mmseq-zlib.patch
+#Fix for C++11 iostream changes
+%patch3 -p1 -b .mmseq-iostream-c++11.patch
 
 #Remove bundled binaries
 rm bin/*-linux
@@ -86,6 +89,9 @@ rm -rf %{buildroot}
 
 
 %changelog
+* Fri Feb 12 2016 Adam Huffman <bloch@verdurin.com> - 1.0.8a-10
+- patch to add compatibility with C++11 iostream
+
 * Wed Feb 10 2016 Adam Huffman <bloch@verdurin.com> - 1.0.8a-9
 - rebuilt to pick up new armadillo