Control: tags -1 patch
Hi Maintainer
I found the Dindel source includes old copies of Boost's foreach.hpp and
digamma.hpp.
The attached patch lets Dindel use the current versions from Boost and
fixes the FTBFS with recent versions of Boost.
Regards
Graham
Description: Use Boost's foreach.hpp instead of embedded copy
This fixes a FTBFS with recent versions of Boost
Bug-Debian: https://bugs.debian.org/833958
Author: Graham Inggs <gin...@debian.org>
Last-Update: 2016-08-19
--- a/DInDel.cpp
+++ b/DInDel.cpp
@@ -24,7 +24,7 @@
#include <boost/math/special_functions/digamma.hpp>
#include <seqan/align.h>
#include <seqan/graph_align.h>
-#include "foreach.hpp"
+#include <boost/foreach.hpp>
#include "bam.h"
#include "DInDel.hpp"
#include "Haplotype.hpp"
--- a/GetCandidates.cpp
+++ b/GetCandidates.cpp
@@ -22,7 +22,7 @@
#include <fstream>
#include <string>
#include "MyBam.hpp"
-#include "foreach.hpp"
+#include <boost/foreach.hpp>
#include "ObservationModelSeqAn.hpp"
#include "GetCandidates.hpp"
#include "Variant.hpp"
@@ -32,7 +32,6 @@
#include "Fasta.hpp"
#include "StringHash.hpp"
#include <set>
-#include "foreach.hpp"
using namespace std;
int GetCandidatesFromCIGAR::getIndelFromCIGARFetchFunc(const bam1_t *b, void *data)
--- a/Haplotype.hpp
+++ b/Haplotype.hpp
@@ -23,7 +23,7 @@
#include <vector>
#include "Variant.hpp"
#include "MLAlignment.hpp"
-#include "foreach.hpp"
+#include <boost/foreach.hpp>
#include <ext/hash_map>
#include <set>
//#include "Fast.hpp"
--- a/OutputData.hpp
+++ b/OutputData.hpp
@@ -25,7 +25,7 @@
#include "StringHash.hpp"
#include <string>
#include <iostream>
-#include "foreach.hpp"
+#include <boost/foreach.hpp>
using namespace std;
using namespace boost;
--- a/StringHash.hpp
+++ b/StringHash.hpp
@@ -25,7 +25,7 @@
#include <ext/hash_map>
#include <string>
#include <iostream>
-#include "foreach.hpp"
+#include <boost/foreach.hpp>
using namespace std;
using namespace boost;
using __gnu_cxx::hash;
--- a/Faster.cpp
+++ b/Faster.cpp
@@ -35,7 +35,7 @@
#include "Haplotype.hpp"
#include "Faster.hpp"
#include "Utils.hpp"
-#include "foreach.hpp"
+#include <boost/foreach.hpp>
using namespace std;
const int DEBUGS=0;
--- a/HaplotypeDistribution.hpp
+++ b/HaplotypeDistribution.hpp
@@ -27,7 +27,7 @@
#include "bam.h"
#include "Haplotype.hpp"
#include "HapBlock.hpp"
-#include "foreach.hpp"
+#include <boost/foreach.hpp>
#include "VariantFile.hpp"
using namespace std;
