25 files changed, 48 insertions, 5953 deletions
diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index ac4304d4e3fb..280297c278fc 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/allpathslg/Manifest b/sci-biology/allpathslg/Manifest
index bfcc1e5cc734..49f0d85cb203 100644
--- a/sci-biology/allpathslg/Manifest
+++ b/sci-biology/allpathslg/Manifest
@@ -1,5 +1,4 @@
-AUX allpathslg-52488_fix-buildsystem.patch 1301 BLAKE2B b478b182a5e34cd462432af3be1432c2d9e4bc876cbf901be56537f842b616fadb767eb7eede3b0ba2a250e83a05dfd4b262b5ce3a0dd17161f0f838b5cc7431 SHA512 f23495515581947761de8b14580b0c28070f38a9a1c9b91403cdf5fbc0efcf48230a3ef7281f9700f0c45b87ceda97733d9329cfacb6112f60fc2f246a0416b9
-AUX allpathslg-52488_remove-namespace-std.patch 49158 BLAKE2B 8779f7ee66bae91d0093afd76e866a1073e97e4dc2bbf9408c5878dec5e582619655d18d05d99bf86900a6951a11bd2b87e7e6837fb96be362c60a8769e071f5 SHA512 e3c918519448c0e37ad57bc90fb6eacad246e53cd759fbf910d725358c1d2e2712f1d1008002e751e0c4decae8a37a5f78e0a0d39dd6a276475aa92cc310d509
-DIST allpathslg-52488.tar.gz 3121949 SHA256 035b49cb21b871a6b111976757d7aee9c2513dd51af04678f33375e620998542 SHA512 c44ef1a3ed5b343bf096663309cc399e79d65e83175232743cf330fd0d426633bd0d388922fd0c73ac0927d85ea9005549c8e4f7711c79fea7107068510ef30d WHIRLPOOL c63a13450c55fce8f2c5399bdd5d8f32939e31d9d13a120835b1d826ae96e251fea81caa134d5d45ad857af0777c22e4ad1d894c81a74db6d83a7d9ad83b12b4
-EBUILD allpathslg-52488-r2.ebuild 1462 BLAKE2B 8a7342d93f34192da2a2097795695ebbc53bd5092d66769acaefdbbc937f2c1841342c280e8decb09478d12607a8df09632706478d177a15150ab6e88374179d SHA512 9e2ae363ed6342015b773de5aba2d62ba30321b1e36d7f9f7bb46dc00592e6d9426291e4dc096ca437640466a4966b65c7217f34a6c5df697c43f43fa5d4c0e8
+DIST allpathslg-52488-patchset.tar.bz2 11405 BLAKE2B 7a4c36884ac95a4eb23291720e422ce1ec41d0bea3a0b10582aa1d8154234971eb8d06979a969e65c1ec1eab031d2500a1ec40809019c8b4aa1d1d2e81427dbe SHA512 a1d58c131afeef04a9d7a2520fcd28a853317323fdcab1a253cb2548546bbc559993c74a68a8032a5d0e865ac2c2d53ff6b4c149aade2d1f87a2ab4116ebe4cc
+DIST allpathslg-52488.tar.gz 3121949 BLAKE2B b75904f9e8256a14c97abae45a0cb41718f95d27a4a072b6144bd125abb57682faa180de6a18399ab4fa43988344c436ca1eab8412433353fcc746c432c33031 SHA512 c44ef1a3ed5b343bf096663309cc399e79d65e83175232743cf330fd0d426633bd0d388922fd0c73ac0927d85ea9005549c8e4f7711c79fea7107068510ef30d
+EBUILD allpathslg-52488-r2.ebuild 1547 BLAKE2B 0ff97cce907b769446002e704f04524450e5370aba0a5f5fcf66313851fa3708e4c204e1dcde637537ebffaa1baf549b7aa1bc097bc293ee9d43488aa952f205 SHA512 39958550cd4ba2d2e17843860a0354f383fe15850b393aa8a48edc76e59307899afedc878ea68f8c2077f720d6e6f631d32ca1b1c11256e5800cb40d6b9027a6
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/allpathslg/allpathslg-52488-r2.ebuild b/sci-biology/allpathslg/allpathslg-52488-r2.ebuild
index e4c4d95288fd..e68430e2462d 100644
--- a/sci-biology/allpathslg/allpathslg-52488-r2.ebuild
+++ b/sci-biology/allpathslg/allpathslg-52488-r2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -8,7 +8,8 @@ inherit autotools flag-o-matic toolchain-funcs
 DESCRIPTION="De novo assembly of whole-genome shotgun microreads"
 # see also http://www.broadinstitute.org/software/allpaths-lg/blog/?page_id=12
 HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd"
-SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/${P}.tar.gz"
+SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/${P}.tar.gz
+	https://dev.gentoo.org/~mgorny/dist/${P}-patchset.tar.bz2"
 
 LICENSE="MIT"
 SLOT="0"
@@ -22,8 +23,8 @@ DEPEND="
 	dev-libs/boost:="
 
 PATCHES=(
-	"${FILESDIR}/${P}_fix-buildsystem.patch"
-	"${FILESDIR}/${P}_remove-namespace-std.patch"
+	"${WORKDIR}/${P}-patchset/${P}_fix-buildsystem.patch"
+	"${WORKDIR}/${P}-patchset/${P}_remove-namespace-std.patch"
 )
 
 pkg_pretend() {
diff --git a/sci-biology/allpathslg/files/allpathslg-52488_fix-buildsystem.patch b/sci-biology/allpathslg/files/allpathslg-52488_fix-buildsystem.patch
deleted file mode 100644
index 7944eb5469dc..000000000000
--- a/sci-biology/allpathslg/files/allpathslg-52488_fix-buildsystem.patch
+++ /dev/null
@@ -1,33 +0,0 @@
-Fix build system to remove hardcoded debugging flags.
-
---- allpathslg-52488/configure.ac
-+++ allpathslg-52488/configure.ac
-@@ -12,7 +12,7 @@
- AC_OPENMP
- AC_OPENMP_CHECK
- 
--CXXFLAGS="$CXXFLAGS -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -ggdb -DNDEBUG"
-+CXXFLAGS="$CXXFLAGS -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG"
- 
- OS_RELEASE="`uname -r`"
- AC_SUBST(CXXFLAGS)
---- allpathslg-52488/m4/broad.m4
-+++ allpathslg-52488/m4/broad.m4
-@@ -35,12 +35,14 @@
-     OLD_CFLAGS=$CFLAGS
-     CFLAGS="$OPENMP_CFLAGS $CFLAGS"
-     AC_MSG_CHECKING([validity of OpenMP configuation.])
--    AC_LINK_IFELSE([#ifndef _OPENMP
-+	AC_LINK_IFELSE([
-+        AC_LANG_SOURCE([[
-+	#ifndef _OPENMP
-      choke me
-     #endif
-     #include <omp.h>
--    int main () { return omp_get_num_threads (); }],
--    [],
-+    int main () { return omp_get_num_threads (); }
-+    ]])],[],
-     [AC_MSG_BROAD_FAIL([Your compiler must support OpenMP.])])
-     CXXFLAGS=$OLD_CXXFLAGS
-     CFLAGS=$OLD_CFLAGS
diff --git a/sci-biology/allpathslg/files/allpathslg-52488_remove-namespace-std.patch b/sci-biology/allpathslg/files/allpathslg-52488_remove-namespace-std.patch
deleted file mode 100644
index 56d04069435c..000000000000
--- a/sci-biology/allpathslg/files/allpathslg-52488_remove-namespace-std.patch
+++ /dev/null
@@ -1,1770 +0,0 @@
-Remove 'using namespace std' causing massive havoc with newly
-introduced std::align in GCC-5. Fix bug
-https://bugs.gentoo.org/show_bug.cgi?id=568440
-
---- allpathslg-52488/src/agp/AgpFile.cc
-+++ allpathslg-52488/src/agp/AgpFile.cc
-@@ -4,6 +4,8 @@
- #include "agp/AgpFile.h"
- #include "TokenizeString.h"
- 
-+using std::cerr;
-+
- char agp_contig::TypeChar_() const
- {
-     switch ( type_ )
---- allpathslg-52488/src/agp/AgpFile.h
-+++ allpathslg-52488/src/agp/AgpFile.h
-@@ -9,6 +9,8 @@
- 
- #include "agp/AgpMods.h"
- 
-+using std::max;
-+
- class agp_entry
- {
-  public:
---- allpathslg-52488/src/agp/AgpMods.cc
-+++ allpathslg-52488/src/agp/AgpMods.cc
-@@ -7,6 +7,8 @@
- 
- #include "system/System.h"
- 
-+using std::istrstream;
-+
- bool 
- agp_mods::SuperShouldBeRemoved( int super_id ) const
- {
---- allpathslg-52488/src/agp/AgpMods.h
-+++ allpathslg-52488/src/agp/AgpMods.h
-@@ -7,6 +7,8 @@
- #include "String.h"
- #include "Vec.h"
- 
-+using std::swap;
-+
- // The class contig_range provides begin and end positions on a
- // contig.  If the end position is before the begin position, the
- // range is considered reversed.  If a length is provided, the range
---- allpathslg-52488/src/allpaths_cache/CacheReadsMerge.cc
-+++ allpathslg-52488/src/allpaths_cache/CacheReadsMerge.cc
-@@ -56,6 +56,8 @@
- #include "feudal/VirtualMasterVec.h"
- #include "random/Shuffle.h"
- 
-+using std::map;
-+
- typedef VirtualMasterVec<BaseVec> VBaseVecVec;
- typedef VirtualMasterVec<QualVec> VQualVecVec;
- 
---- allpathslg-52488/src/AnAssemblyClass.h
-+++ allpathslg-52488/src/AnAssemblyClass.h
-@@ -19,6 +19,8 @@
- #include "ReadLocation.h"
- #include "ReadPairing.h"
- 
-+using std::map;
-+
- class assembly;
- 
- class super {
---- allpathslg-52488/src/efasta/EfastaTools.cc
-+++ allpathslg-52488/src/efasta/EfastaTools.cc
-@@ -19,6 +19,8 @@
- #include "math/Array.h"
- #include <iostream>
- 
-+using std::set;
-+
- #define Err(message)                                      \
- {    cout << message << endl << "\nInvalid.\n" << endl;   \
-      TracebackThisProcess( );    }
---- allpathslg-52488/src/Equiv.cc
-+++ allpathslg-52488/src/Equiv.cc
-@@ -9,6 +9,8 @@
- #include "Equiv.h"
- #include "Vec.h"
- 
-+using std::swap;
-+
- bool equivalence_relation::equiv(int a, int b) const
- {    if ( a == b ) return true;
-      int c = a;
---- allpathslg-52488/src/FastaFilestream.cc
-+++ allpathslg-52488/src/FastaFilestream.cc
-@@ -13,6 +13,8 @@
- 
- #include <strstream>
- 
-+using std::string;
-+
- template <typename vecT, typename seqT, typename convT, typename verifT>
- FastaFilestream<vecT,seqT,convT,verifT>::FastaFilestream( const String& filename,
-                                                           FastaNameParser* name_parser )
---- allpathslg-52488/src/FastaFilestreamPreview.cc
-+++ allpathslg-52488/src/FastaFilestreamPreview.cc
-@@ -11,6 +11,8 @@
- 
- #include <algorithm>
- 
-+using std::streamoff;
-+
- FastaFilestreamPreview::FastaFilestreamPreview(istream& filestream)
-   : max_sequence_size_(0), start_offset_(0)
- {
---- allpathslg-52488/src/FastaFilestreamPreview.h
-+++ allpathslg-52488/src/FastaFilestreamPreview.h
-@@ -12,6 +12,8 @@
- 
- #include "Vec.h"
- 
-+using std::streampos;
-+
- // FastaFilestreamPreview understands just enough about the fasta
- // format to be able to count the number of sequences in the specified
- // filestream and to know where each sequence starts in that filestream.
---- allpathslg-52488/src/Fastavector.cc
-+++ allpathslg-52488/src/Fastavector.cc
-@@ -14,6 +14,8 @@
- #include <istream>
- #include <string>
- 
-+using std::max;
-+
- // Split this into chunks, separated by gaps ('n'), and return each chunk as a
- // gapless fastavector.
- // TODO: generalize this into a templatized STL algorithm.
---- allpathslg-52488/src/Fastavector.h
-+++ allpathslg-52488/src/Fastavector.h
-@@ -24,6 +24,9 @@
- #include <iostream>
- #include <unistd.h>
- 
-+using std::string;
-+using std::istringstream;
-+
- typedef std::tuple<String, int, int> FastaRegion;
- 
- class fastaindex {
---- allpathslg-52488/src/FetchReads.cc
-+++ allpathslg-52488/src/FetchReads.cc
-@@ -36,6 +36,8 @@
- #include "Qualvector.h"
- #include "random/Random.h"
- 
-+using std::istringstream;
-+
- // Heuristic constants:
- 
- namespace
---- allpathslg-52488/src/feudal/BaseVec.cc
-+++ allpathslg-52488/src/feudal/BaseVec.cc
-@@ -21,6 +21,7 @@
- using std::ostream;
- using std::cout;
- using std::endl;
-+using std::max_element;
- 
- // Cap: in a given basevector, replace any sequence of N > n identical
- // bases by n of the same base.
---- allpathslg-52488/src/graph/Digraph.cc
-+++ allpathslg-52488/src/graph/Digraph.cc
-@@ -17,6 +17,9 @@
- #include "graph/Digraph.h"
- #include "math/Functions.h"
- 
-+using std::make_pair;
-+using std::priority_queue;
-+
- void digraph::TransferEdges( int v, int w, const Bool enter_only )
- {    ForceAssert( v != w );
- 
---- allpathslg-52488/src/graph/Digraph.h
-+++ allpathslg-52488/src/graph/Digraph.h
-@@ -52,6 +52,8 @@
- #include "system/TraceVal.h"
- #include <cstddef>
- 
-+using std::function;
-+
- typedef pair<int, int> VertexPair;
- 
- typedef int vrtx_t;
---- allpathslg-52488/src/graph/DigraphTemplate.h
-+++ allpathslg-52488/src/graph/DigraphTemplate.h
-@@ -34,6 +34,8 @@
- #include "graph/Digraph.h"
- #include <cstddef>
- 
-+using std::make_pair;
-+
- template<class E> vec<int> digraphE<E>:: EdgesBoundedBy( const int e1, const int e2,
-      const vec<int>& to_left, const vec<int>& to_right ) const
- {    int v = to_right[e1], w = to_left[e2];
---- allpathslg-52488/src/graph/GraphAlgorithms.h
-+++ allpathslg-52488/src/graph/GraphAlgorithms.h
-@@ -9,7 +9,7 @@
- #ifndef GRAPH__GRAPH_ALGORITHMS__H_
- #define GRAPH__GRAPH_ALGORITHMS__H_
- 
--
-+using std::map;
- 
- // -------------- Union Find ---------------
- //
---- allpathslg-52488/src/IndexedAlignmentPlusVector.h
-+++ allpathslg-52488/src/IndexedAlignmentPlusVector.h
-@@ -15,6 +15,8 @@
- 
- #include "Alignment.h"
- 
-+using std::streampos;
-+using std::streamoff;
- 
- // This class encapsulates the header information for both vectors and indices.
- 
---- allpathslg-52488/src/kmers/kmer_parcels/KmerParcelsClasses.h
-+++ allpathslg-52488/src/kmers/kmer_parcels/KmerParcelsClasses.h
-@@ -6,6 +6,9 @@
- //   Institute is not responsible for its use, misuse, or functionality.     //
- ///////////////////////////////////////////////////////////////////////////////
- 
-+using std::hex;
-+using std::dec;
-+
- // ---------------------------------
- // NaifTimer
- // ---------------------------------
---- allpathslg-52488/src/kmers/naif_kmer/KernelErrorFinder.h
-+++ allpathslg-52488/src/kmers/naif_kmer/KernelErrorFinder.h
-@@ -13,8 +13,8 @@
- #include "kmers/naif_kmer/LockedBlocks.h"
- #include "kmers/naif_kmer/Kmers.h"
- 
--
--
-+using std::make_pair;
-+using std::stringstream;
- 
- 
- 
---- allpathslg-52488/src/kmers/naif_kmer/Kmers.h
-+++ allpathslg-52488/src/kmers/naif_kmer/Kmers.h
-@@ -14,7 +14,7 @@
- 
- #include "kmers/naif_kmer/KmerFunctions.h"
- 
--
-+using std::string;
- 
- // ---- 256 random 64bit numbers to compute hash key 
- 
---- allpathslg-52488/src/layout/ContigActualloc.h
-+++ allpathslg-52488/src/layout/ContigActualloc.h
-@@ -17,6 +17,8 @@
- #include "system/Crash.h"
- #include "Misc.h"
- 
-+using std::set;
-+using std::map;
- 
- //
- // Class contig_actualloc
---- allpathslg-52488/src/lookup/ImperfectLookup.h
-+++ allpathslg-52488/src/lookup/ImperfectLookup.h
-@@ -51,6 +51,8 @@
- #include "lookup/LookupTools.h"
- #include "lookup/AlignCollector.h"
- 
-+using std::auto_ptr;
-+
- class TaskTimer;
- 
- 
---- allpathslg-52488/src/lookup/LookAlign.cc
-+++ allpathslg-52488/src/lookup/LookAlign.cc
-@@ -29,6 +29,8 @@
- #include "random/Random.h"
- #include "system/ParsedArgs.h"
- 
-+using std::istrstream;
-+
- String QUERY("QUERY");
- 
- void look_align::ResetFromAlign(const align & al, const basevector & b1,
---- allpathslg-52488/src/lookup/LookupTable.h
-+++ allpathslg-52488/src/lookup/LookupTable.h
-@@ -18,6 +18,8 @@
- 
- #include <set>
- 
-+using std::set;
-+
- typedef pair<unsigned int, unsigned int> LocSeq;
- 
- ///
---- allpathslg-52488/src/lookup/QueryLookupTableCore.cc
-+++ allpathslg-52488/src/lookup/QueryLookupTableCore.cc
-@@ -465,6 +465,9 @@
- #include "system/ParsedArgs.h"
- #include "system/file/FileReader.h"
- 
-+using std::istrstream;
-+using std::less_equal;
-+
- #define ABORT(MSG)                                 \
- {    out << MSG << "  Abort." << endl << endl;     \
-      exit(1);    }
---- allpathslg-52488/src/lookup/ShortQueryLookup.cc
-+++ allpathslg-52488/src/lookup/ShortQueryLookup.cc
-@@ -32,6 +32,8 @@
- #include "lookup/AlignCollector.h"
- #include "lookup/ImperfectLookup.h"
- 
-+using std::ios_base;
-+
- // Run an alignment processing chain: seqs -> look -> receiver -> aligns
- // That is, look turns seqs into hits, which receiver accepts
- // and turns into alignments which are passed to aligns.  The
---- allpathslg-52488/src/Map.h
-+++ allpathslg-52488/src/Map.h
-@@ -23,7 +23,7 @@
- #include <unordered_map>
- #include <ext/hash_map>
- using namespace __gnu_cxx;
--
-+using std::map;
- 
- template <class K, class V, class C=std::less<K>>
- using StdMap = std::map<K,V,C,typename DefaultAllocator<std::pair<K const,V>>::type>;
---- allpathslg-52488/src/math/Array.h
-+++ allpathslg-52488/src/math/Array.h
-@@ -13,6 +13,8 @@
- #include "Vec.h"
- #include "Map.h"
- 
-+using std::fill;
-+
- // ==============================================================================
- // A fixed-size simple c-style 2D array that allocates faster than vec< vec<T> >
- // The elements are uninitialized.
---- allpathslg-52488/src/math/Functions.cc
-+++ allpathslg-52488/src/math/Functions.cc
-@@ -10,7 +10,7 @@
- #include "STLExtensions.h"
- #include "math/Functions.h"
- 
--
-+using std::make_pair;
- 
- 
- /*  CombineNormalDistribution              Filipe Ribeiro 2009-06-22
---- allpathslg-52488/src/math/Functions.h
-+++ allpathslg-52488/src/math/Functions.h
-@@ -15,6 +15,10 @@
- #include <cmath>
- #include <numeric>
- 
-+using std::min;
-+using std::cerr;
-+using std::swap;
-+
- // ===========================================================================
- //
- // Min functions
---- allpathslg-52488/src/math/HoInterval.cc
-+++ allpathslg-52488/src/math/HoInterval.cc
-@@ -10,6 +10,8 @@
- #include "math/HoInterval.h"
- #include "STLExtensions.h"
- 
-+using std::make_pair;
-+
- bool ho_interval::Merge(const ho_interval & o) {
-   if (!Meets(*this,o)) return false;
-   *this = Span(*this, o);
---- allpathslg-52488/src/math/HoInterval.h
-+++ allpathslg-52488/src/math/HoInterval.h
-@@ -14,6 +14,8 @@
- #include "feudal/MasterVec.h"
- #include "feudal/SerfVec.h"
- 
-+using std::max;
-+
- /// Class: ho_interval
- /// A half-open interval [a, b).
- class ho_interval {
---- allpathslg-52488/src/math/IntFunction.h
-+++ allpathslg-52488/src/math/IntFunction.h
-@@ -21,6 +21,8 @@
- 
- #include "MainTools.h"
- 
-+using std::deque;
-+using std::fixed;
- 
- #define __INT_FUNCTION_BINARY_VERSION__ 2
- 
---- allpathslg-52488/src/PackAlign.h
-+++ allpathslg-52488/src/PackAlign.h
-@@ -133,6 +133,8 @@
- #include "pairwise_aligners/Mutmer.h"
- #include "feudal/BinaryStream.h"
- 
-+using std::make_pair;
-+
- const int Bits2  = 3, Bits3  = 7, Bits4 = 15, Bits10 = 1023, Bits12 = 4095, 
-   Bits16 = 65535;
- 
---- allpathslg-52488/src/PairsManager.h
-+++ allpathslg-52488/src/PairsManager.h
-@@ -61,6 +61,7 @@
- #include "feudal/BinaryStream.h"
- #include <cstddef>
- 
-+using std::make_pair;
- 
- class PairsManager; // forward declaration
- 
---- allpathslg-52488/src/pairwise_aligners/MakeAlignsMethod.cc
-+++ allpathslg-52488/src/pairwise_aligners/MakeAlignsMethod.cc
-@@ -19,6 +19,9 @@
- #include "pairwise_aligners/AlignFromMutmers.h"
- #include "pairwise_aligners/SmithWatBandedA.h"
- 
-+using std::map;
-+using std::set;
-+
- // If there's a perfect match of length at least perf but we produced no proper 
- // alignment, use banded Smith-Waterman to create one.
- 
---- allpathslg-52488/src/pairwise_aligners/MatchList.cc
-+++ allpathslg-52488/src/pairwise_aligners/MatchList.cc
-@@ -9,6 +9,8 @@
- 
- #include "pairwise_aligners/MatchList.h"
- 
-+using std::max;
-+
- bool MatchList::FindMatchInSorted( const int id1, const Match& newMatch ) const 
- {
-   const vec<Match>& sortedMatches = m_sortedMatches[id1];
---- allpathslg-52488/src/paths/AlignHyperKmerPath.cc
-+++ allpathslg-52488/src/paths/AlignHyperKmerPath.cc
-@@ -23,6 +23,9 @@
- #include "paths/KmerBaseBroker.h"
- #include "paths/KmerPath.h"
- 
-+using std::ostringstream;
-+using std::set;
-+
- // Function: AlignHyperKmerPath
- //
- // AlignHyperKmerPath takes a HyperKmerPath h, whose KmerPath edges are assumed
---- allpathslg-52488/src/paths/CAltFasta.cc
-+++ allpathslg-52488/src/paths/CAltFasta.cc
-@@ -11,7 +11,7 @@
- #include "paths/FixSomeIndelsUtils.h"
- #include "efasta/EfastaTools.h"
- 
--
-+using std::set;
- 
- /**
-  * CAltFasta
---- allpathslg-52488/src/paths/ChangeLibraryStats.cc
-+++ allpathslg-52488/src/paths/ChangeLibraryStats.cc
-@@ -47,8 +47,10 @@
-     
-     int libID = pairs.libraryID( libName );
-     ForceAssertLt( libID, nLibraries); ForceAssertGe( libID, 0 );
--    cout << "old: " << PRINT4( libName, libID, pairs.getLibrarySep(libID), pairs.getLibrarySD(libID) );
--    cout << "new: " << PRINT4( libName, libID, sep, dev );
-+    cout << "old: ";
-+	PRINT4( libName, libID, pairs.getLibrarySep(libID), pairs.getLibrarySD(libID) );
-+    cout << "new: ";
-+	PRINT4( libName, libID, sep, dev );
-     pairs.changeLibrarySepSd( libID, sep, dev );
-   }
-   in.close();
---- allpathslg-52488/src/paths/CorrectLongReadsTools.h
-+++ allpathslg-52488/src/paths/CorrectLongReadsTools.h
-@@ -16,6 +16,8 @@
- #include "paths/LongReadTools.h"
- #include "paths/Uniseq.h"
- 
-+using std::map;
-+
- class heuristics {
- 
-      public:
---- allpathslg-52488/src/paths/ExtendUnipathSeqs.cc
-+++ allpathslg-52488/src/paths/ExtendUnipathSeqs.cc
-@@ -13,6 +13,9 @@
- 
- #include <set>
- 
-+using std::set;
-+using std::back_inserter;
-+
- void ExtendUnipathSeqs( const vecKmerPath& unipaths,
-                         const vecUnipathSeq& unipathSeqs,
-                         vecUnipathSeq& extendedUnipathSeqs,
---- allpathslg-52488/src/paths/FindErrorsCore.cc
-+++ allpathslg-52488/src/paths/FindErrorsCore.cc
-@@ -20,6 +20,8 @@
- #include "kmers/naif_kmer/KernelPreCorrector.h"
- #include "system/WorklistN.h"
- 
-+using std::map;
-+
- static inline 
- String Tag(String S = "FEC") { return Date() + " (" + S + "): "; } 
- 
---- allpathslg-52488/src/paths/FindErrorsCore.h
-+++ allpathslg-52488/src/paths/FindErrorsCore.h
-@@ -14,7 +14,7 @@
- 
- #include "kmers/KmerSpectra.h"
- 
--
-+using std::set;
- 
- class PC_Params
- {
---- allpathslg-52488/src/paths/FindUnipathSeedsLG.cc
-+++ allpathslg-52488/src/paths/FindUnipathSeedsLG.cc
-@@ -16,6 +16,8 @@
- #include "paths/simulation/Placement.h"
- #include <thread>
- 
-+using std::ostringstream;
-+
- // A whole bunch of variables that are shared by parallel threads.
- 
- static const digraphE<fsepdev>* FG_ptr;
---- allpathslg-52488/src/paths/FindUnipathSeedsLG.h
-+++ allpathslg-52488/src/paths/FindUnipathSeedsLG.h
-@@ -19,7 +19,7 @@
- #include "paths/simulation/Placement.h" // placement
- #include "paths/UnipathNhoodLG.h" // sepdev, fsepdev
- 
--
-+using std::string;
- 
- enum SeedStatus
-   { SEED_GOOD, SEED_ISOLATED, SEED_SHORT, SEED_HIGH_CN, SEED_ZERO_CN, SEED_RC_ON_REF, SEED_REDUNDANT, SEED_RC_OF_SEED };
---- allpathslg-52488/src/paths/FixLocal.cc
-+++ allpathslg-52488/src/paths/FixLocal.cc
-@@ -88,6 +88,8 @@
- #include "paths/Unipath.h"
- #include "paths/FindErrorsCore.h"
- 
-+using std::ostringstream;
-+
- void AddToPileup( const read_loc& rl, const basevector& b, const qualvector& q,
-      const basevector& tig, vec<dumbcall>& calls )
- {    align a;
---- allpathslg-52488/src/paths/FragmentFillerDefs.h
-+++ allpathslg-52488/src/paths/FragmentFillerDefs.h
-@@ -28,6 +28,8 @@
- #include <set>
- #include <time.h>
- 
-+using std::map;
-+
- namespace
- {
- 
---- allpathslg-52488/src/paths/GetHomes.cc
-+++ allpathslg-52488/src/paths/GetHomes.cc
-@@ -17,6 +17,8 @@
- #include "paths/Uniseq.h"
- #include "util/SearchFastb2Core.h"
- 
-+using std::ostringstream;
-+
- class vepath {
- 
-      public:
---- allpathslg-52488/src/paths/HyperFastavector.cc
-+++ allpathslg-52488/src/paths/HyperFastavector.cc
-@@ -14,6 +14,8 @@
- #include "feudal/BinaryStream.h"
- #include <thread>
- 
-+using std::ostringstream;
-+
- // Order a pair of vec<int>s lexicographically using subset relation.
- 
- struct order_vecint_binsubset_pair
---- allpathslg-52488/src/paths/HyperKmerPathCleaner.cc
-+++ allpathslg-52488/src/paths/HyperKmerPathCleaner.cc
-@@ -11,6 +11,7 @@
- #include "paths/HyperKmerPathCleaner.h"
- #include <set>
- 
-+using std::set;
- 
- void HyperKmerPathCleaner::CleanUpGraph( HyperKmerPath& ans ) const {
- 
---- allpathslg-52488/src/paths/InsertWalker.h
-+++ allpathslg-52488/src/paths/InsertWalker.h
-@@ -34,7 +34,7 @@
- #include "paths/KmerPath.h"
- #include "TaskTimer.h" // TaskTimer
- 
--
-+using std::set;
- 
- 
- 
---- allpathslg-52488/src/paths/InternalMergeImpl.cc
-+++ allpathslg-52488/src/paths/InternalMergeImpl.cc
-@@ -17,7 +17,7 @@
- #include "paths/InternalMergeImpl.h"
- #include "graph/Digraph.h"
- 
--
-+using std::set;
- 
- 
- /*******************************************************************************
---- allpathslg-52488/src/paths/KmerAlignSet.h
-+++ allpathslg-52488/src/paths/KmerAlignSet.h
-@@ -12,6 +12,8 @@
- #include "Basevector.h"
- #include "CoreTools.h"
- 
-+using std::make_pair;
-+
- // KmerAlignSet.  It represents a set of alignments of a read to unibases, although
- // in principle the 'read' could be any sequence and the 'unibases' could be any set
- // of sequences.
---- allpathslg-52488/src/paths/KmerBaseBroker.h
-+++ allpathslg-52488/src/paths/KmerBaseBroker.h
-@@ -20,6 +20,8 @@
- #include <algorithm>  // for set_union
- #include <map>
- 
-+using std::map;
-+
- /**
-    Class: KmerBaseBrokerTemplate
- 
---- allpathslg-52488/src/paths/KmerPathDatabase.cc
-+++ allpathslg-52488/src/paths/KmerPathDatabase.cc
-@@ -4,6 +4,8 @@
- #include "feudal/BinaryStream.h"
- #include <map>
- 
-+using std::map;
-+
- // Methods of class KmerPathDatabaseTemplate.
- 
- template <class TAG>
---- allpathslg-52488/src/paths/KmerPath.h
-+++ allpathslg-52488/src/paths/KmerPath.h
-@@ -22,6 +22,8 @@
- #include "HashSimple.h"
- #include "graph/Digraph.h"
- 
-+using std::make_pair;
-+
- class KmerPathLoc;  // forward declaration
- 
- /**
---- allpathslg-52488/src/paths/KmerPathInterval.cc
-+++ allpathslg-52488/src/paths/KmerPathInterval.cc
-@@ -128,11 +128,11 @@
- }
- 
- template void Contains( const vec<tagged_rpint>& segs, kmer_id_t index, 
--               vec<longlong>& answer, bool append, int cap );
-+               vec<longlong>& answer, bool append = false, int cap = -1 );
- template void Contains( const vec<big_tagged_rpint>& segs, kmer_id_t index, 
--               vec<longlong>& answer, bool append, int cap );
-+               vec<longlong>& answer, bool append = false, int cap = -1 );
- template void Contains( const vec<new_tagged_rpint>& segs, kmer_id_t index, 
--               vec<longlong>& answer, bool append, int cap );
-+               vec<longlong>& answer, bool append = false, int cap = -1 );
- 
- // Overload Contains() with a second version that looks for all intervals overlapping
- // a given KmerPathInterval, instead of a single kmer.
-@@ -203,11 +203,11 @@
- }
- 
- template void Contains( const vec<tagged_rpint>& segs, KmerPathInterval rpi, 
--     vec<longlong>& answer, bool append, int cap );
-+     vec<longlong>& answer, bool append = false, int cap = -1 );
- template void Contains( const vec<big_tagged_rpint>& segs, KmerPathInterval rpi, 
--     vec<longlong>& answer, bool append, int cap );
-+     vec<longlong>& answer, bool append = false, int cap = -1 );
- template void Contains( const vec<new_tagged_rpint>& segs, KmerPathInterval rpi, 
--     vec<longlong>& answer, bool append, int cap );
-+     vec<longlong>& answer, bool append = false, int cap = -1 );
- 
- // This will efficiently find a single instance of the requested kmer.  
- // Intended for base lookup, where you don't need to find all of them.
---- allpathslg-52488/src/paths/KmerPathInterval.h
-+++ allpathslg-52488/src/paths/KmerPathInterval.h
-@@ -8,6 +8,8 @@
- #include "CommonSemanticTypes.h"
- #include "feudal/BinaryStreamTraits.h"
- 
-+using std::max;
-+
- // Portability note: endianness
- // The implementations here would need to be changed for big endian architectures.
- 
-@@ -116,6 +118,15 @@
-    To do: check that "gaps in kmer paths are not used for assembly from short reads"
-    is true.
- */
-+
-+class KmerPathInterval;
-+
-+template<class TAG>
-+void Contains( const vec<TAG>& segs, kmer_id_t index, vec<longlong>& answer, bool append = false, int cap = -1 );
-+
-+template<class TAG>
-+void Contains( const vec<TAG>& segs, KmerPathInterval rpi, vec<longlong>& answer, bool append = false, int cap = -1 );
-+
- class KmerPathInterval {
-  public:
-   KmerPathInterval( ) { }
-@@ -364,11 +375,11 @@
- 
-      template<class TAG>
-      friend void Contains( const vec<TAG>& segs, kmer_id_t index,
--          vec<longlong>& answer, bool append = false, int cap = -1 );
-+          vec<longlong>& answer, bool append, int cap );
- 
-      template<class TAG>
-      friend void Contains( const vec<TAG>& segs, KmerPathInterval rpi,
--          vec<longlong>& answer, bool append = false, int cap = -1 );
-+          vec<longlong>& answer, bool append, int cap );
- 
-      template<class TAG>
-      friend longlong Instance( const vec<TAG>& segs, kmer_id_t k );
-@@ -491,11 +502,11 @@
- 
-      template<class TAG>
-      friend void Contains( const vec<TAG>& segs, kmer_id_t index,
--          vec<longlong>& answer, bool append = false, int cap = -1 );
-+          vec<longlong>& answer, bool append, int cap );
- 
-      template<class TAG>
-      friend void Contains( const vec<TAG>& segs, KmerPathInterval rpi,
--          vec<longlong>& answer, bool append = false, int cap = -1 );
-+          vec<longlong>& answer, bool append, int cap );
- 
-      template<class TAG>
-      friend longlong Instance( const vec<TAG>& segs, kmer_id_t k );
-@@ -622,11 +633,11 @@
- 
-      template<class TAG>
-      friend void Contains( const vec<TAG>& segs, kmer_id_t index,
--          vec<longlong>& answer, bool append = false, int cap = -1 );
-+          vec<longlong>& answer, bool append, int cap );
- 
-      template<class TAG>
-      friend void Contains( const vec<TAG>& segs, KmerPathInterval rpi,
--          vec<longlong>& answer, bool append = false, int cap = -1 );
-+          vec<longlong>& answer, bool append, int cap );
- 
-      template<class TAG>
-      friend kmer_id_t Instance( const vec<TAG>& segs, kmer_id_t k );
---- allpathslg-52488/src/paths/KPatch.cc
-+++ allpathslg-52488/src/paths/KPatch.cc
-@@ -32,6 +32,8 @@
- #include "paths/AssemblyEdit.h"
- #include "paths/GetNexts.h"
- 
-+using std::ostringstream;
-+
- template<int K> void PatchMe( const vec<basevector>& jbases_sorted,
-      const vec<int64_t>& jbases_sorted_id, const PairsManager& jpairs,
-      const vec< triple<int64_t,int,int> >& jaligns, const vec<superb>& scaffolds,
---- allpathslg-52488/src/paths/LinkingPairs.cc
-+++ allpathslg-52488/src/paths/LinkingPairs.cc
-@@ -9,6 +9,8 @@
- #include "paths/LinkingPairs.h"
- #include "math/Array.h"
- 
-+using std::multiset;
-+
- void LinkingPairs::Init(int nlibs_, const vec<int>& lens )
- {
-   nlibs = nlibs_;
---- allpathslg-52488/src/paths/long/EvalByReads.cc
-+++ allpathslg-52488/src/paths/long/EvalByReads.cc
-@@ -19,6 +19,8 @@
- #include <queue>
- #include <omp.h>
- 
-+using std::priority_queue;
-+
- namespace {
-     struct CompareReadPlaceByQsum {
-         bool operator() (const read_place& a, const read_place& b) 
---- allpathslg-52488/src/paths/long/EvalCorrected.cc
-+++ allpathslg-52488/src/paths/long/EvalCorrected.cc
-@@ -25,6 +25,8 @@
- #include "paths/long/MakeKmerStuff.h"
- #include "random/Random.h"
- 
-+using std::set;
-+
- void EvalCorrected( 
-      const VecEFasta& corrected0,             // corrected reads
-      const vec<int>& cid,                     // ids of corrected reads
---- allpathslg-52488/src/paths/long/fosmid/Fosmids.cc
-+++ allpathslg-52488/src/paths/long/fosmid/Fosmids.cc
-@@ -15,6 +15,9 @@
- #include "paths/long/fosmid/Fosmids.h"
- #include "math/HoInterval.h"
- 
-+using std::istringstream;
-+using std::ostringstream;
-+
- vec<int> ChrSizes(void)
- {
-      return {249250621,243199373,198022430,191154276,180915260,171115067,
---- allpathslg-52488/src/paths/long/KmerAlign.cc
-+++ allpathslg-52488/src/paths/long/KmerAlign.cc
-@@ -12,6 +12,8 @@
- #include "Equiv.h"
- #include "VecUtilities.h"
- 
-+using std::map;
-+
- void KmerAlign( 
-         const vec< pair<int,int> > & offset, 
-         vec< pair<int,int> > & aligns,
---- allpathslg-52488/src/paths/long/OverlapReads.cc
-+++ allpathslg-52488/src/paths/long/OverlapReads.cc
-@@ -10,6 +10,10 @@
- #include "FeudalMimic.h"
- #include <queue>
- 
-+using std::max;
-+using std::queue;
-+using std::make_pair;
-+
- // ================================ static methods =============================
- 
- // If tail b1[len1-overlap:len1) is the same as head b2[0: overlap)
---- allpathslg-52488/src/paths/long/RefTraceTools.cc
-+++ allpathslg-52488/src/paths/long/RefTraceTools.cc
-@@ -10,6 +10,8 @@
- #include "VecUtilities.h"
- #include "math/HoInterval.h"
- 
-+using std::get;
-+
- void CreateHBPlus(const HyperBasevector& hb, const vec<int>& inv,
-         HyperBasevector& hbp, vec<pair<int,Bool>>& hbp_to_hb) 
- {
---- allpathslg-52488/src/paths/long/ultra/ConsensusScoreModel.cc
-+++ allpathslg-52488/src/paths/long/ultra/ConsensusScoreModel.cc
-@@ -12,6 +12,8 @@
- #include "VecUtilities.h"
- #include <map>
- 
-+using std::map;
-+
- ConsensusScoreModel::ConsensusScoreModel( double del_rate, double ins_rate, double sub_rate,
-        bool ignore_matching_score, bool score_fast )
- {
---- allpathslg-52488/src/paths/long/VariantCallTools.cc
-+++ allpathslg-52488/src/paths/long/VariantCallTools.cc
-@@ -27,6 +27,8 @@
- #include "paths/long/VariantReadSupport.h"
- #include "kmers/KMer.h"
- 
-+using std::stack;
-+
- namespace {
- 
- bool IsBubbleEdge(int eid, const HyperBasevector& hb, const vec<int>& to_left,
---- allpathslg-52488/src/paths/long/VariantReadSupport.cc
-+++ allpathslg-52488/src/paths/long/VariantReadSupport.cc
-@@ -23,6 +23,13 @@
- #include "paths/long/ReadOriginTracker.h"
- #include "paths/long/EvalByReads.h"
- 
-+#include <cmath>
-+
-+using std::get;
-+using std::make_tuple;
-+using std::ignore;
-+using std::tie;
-+
- namespace {
- void CalcLengthProbSimple(vec<double>&vOut,const double dProbIns_len, const double dProbDel_len, const uint64_t org_length){
-     const double dProbIns=dProbIns_len;
-@@ -158,7 +165,7 @@
-     for(uint64_t ff=1;ff<nFlavors;++ff){
-         for( size_t ll = 2 ; ll <= get<0>(n_q_len[ff]) ; ++ll){ dFactor /= (long double)(ll); }
-     }
--    if( dFactor==std::numeric_limits<long double>::infinity() || isnan(dFactor) ){ dFactor=1.0; }
-+    if( dFactor==std::numeric_limits<long double>::infinity() || std::isnan(dFactor) ){ dFactor=1.0; }
-     if(verbosity>0) std::cout << "dFactor " << dFactor << std::endl;
- 
-     long double dDenom=0.0;
-@@ -193,7 +200,7 @@
-         }
-     }
-     if(verbosity>0) std::cout <<"denom: " << dDenom<< std::endl;
--    if( dDenom < std::numeric_limits<long double>::epsilon() * 100 || isnan(dDenom)) return;
-+    if( dDenom < std::numeric_limits<long double>::epsilon() * 100 || std::isnan(dDenom)) return;
-     ForceAssert(dDenom>0);
-     if(verbosity>0){
-         for( uint64_t row=0;row<nFlavors;++row){
---- allpathslg-52488/src/paths/long/VariantReadSupport.h
-+++ allpathslg-52488/src/paths/long/VariantReadSupport.h
-@@ -5,6 +5,8 @@
- #include "Qualvector.h"
- #include "paths/HyperBasevector.h"
- 
-+using std::tuple;
-+
- // forward declaration
- class read_place;
- class ReadOriginTracker;
---- allpathslg-52488/src/paths/long/Variants.cc
-+++ allpathslg-52488/src/paths/long/Variants.cc
-@@ -22,6 +22,8 @@
- #include "paths/long/VariantFilters.h"
- #include "paths/long/VariantPostProcess.h"
- 
-+using std::set;
-+
- int MarkVariants( HyperEfasta& he, const vec<VariantSignature>& v_signatures,
-      const long_logging& logc )
- {    double clock = WallClockTime( );
---- allpathslg-52488/src/paths/LongReadTools.h
-+++ allpathslg-52488/src/paths/LongReadTools.h
-@@ -17,6 +17,8 @@
- #include "kmers/KmerRecord.h"
- #include "paths/AssemblyEdit.h"
- 
-+using std::ostringstream;
-+
- // A gap patcher is defined by left and right ints u1 and u2, and a BaseVec r,
- // whose left end aligns to u1 starting at tpos1 and whose right end aligns to u2
- // ending at tpos2, where the positions are in terms of the BaseVecs associated
---- allpathslg-52488/src/paths/MakeScaffoldsCloseBest.cc
-+++ allpathslg-52488/src/paths/MakeScaffoldsCloseBest.cc
-@@ -29,6 +29,8 @@
- #include "paths/reporting/CLinkBundle.h"
- #include <sstream>
- 
-+using std::ostringstream;
-+
- // An slink is a link between scaffolds.  The first scaffold is not represented
- // in the object.
- 
---- allpathslg-52488/src/paths/Mixmer.cc
-+++ allpathslg-52488/src/paths/Mixmer.cc
-@@ -73,6 +73,9 @@
- #include "util/ReadTracker.h"
- #include "util/SearchFastb2Core.h"
- 
-+using std::ostringstream;
-+using std::istrstream;
-+
- // CorrectErrors.
- 
- void CorrectErrors( vecbasevector& bases, vecqualvector& quals,
---- allpathslg-52488/src/paths/MuxGraph.cc
-+++ allpathslg-52488/src/paths/MuxGraph.cc
-@@ -6,6 +6,7 @@
- 
- #include <set>
- 
-+using std::set;
- 
- // Functions to translate pathIds to nodeIds and back.
- 
---- allpathslg-52488/src/paths/MuxSearchAgent.h
-+++ allpathslg-52488/src/paths/MuxSearchAgent.h
-@@ -15,6 +15,10 @@
- #include "paths/MuxSearchState.h"
- #include "paths/MuxSearchPolicy.h"
- 
-+using std::hex;
-+using std::dec;
-+using std::mem_fun;
-+
- /// The search agent directed by the SearchDirector of a
- /// KmerPathMuxSearcher.
- ///
---- allpathslg-52488/src/paths/MuxSearchPolicy.h
-+++ allpathslg-52488/src/paths/MuxSearchPolicy.h
-@@ -29,6 +29,7 @@
- #include <hash_set>
- #endif
- 
-+using std::map;
- 
- ////////////////////////////////////////////////////////////////////////////
- ///
---- allpathslg-52488/src/paths/OffsetTracker.cc
-+++ allpathslg-52488/src/paths/OffsetTracker.cc
-@@ -10,6 +10,8 @@
- #include "paths/OffsetTracker.h"
- #include <queue>
- 
-+using std::priority_queue;
-+
- MutableOffsetTracker::MutableOffsetTracker( const vecUnipathSeq& unipathSeqs, 
-                                             const MuxGraph& inverseMuxGraph,
-                                             const int firstSuperSeq,
---- allpathslg-52488/src/paths/PairDistFitting.h
-+++ allpathslg-52488/src/paths/PairDistFitting.h
-@@ -38,7 +38,7 @@
- //
- template <class T>
- void MostProbableGap( const T& distr, const int len1, const int len2, const vec< pair< int, int > >& links, 
--    int& gap, int& std, bool verbose=false )
-+    int& gap, int& std, bool verbose )
- {
-   ForceAssertGt( links.isize(), 0 );
-   // find the averge of x1 + x2 ( <x1+x2> = <L> - g in the ideal case )
---- allpathslg-52488/src/paths/PairDistModels.h
-+++ allpathslg-52488/src/paths/PairDistModels.h
-@@ -23,6 +23,8 @@
- #include <map>
- #include "math/IntDistribution.h"
- 
-+using std::map;
-+
- // =====================================================
- // Class ProbFuncInterface
- //
---- allpathslg-52488/src/paths/PatcherCottageCore.cc
-+++ allpathslg-52488/src/paths/PatcherCottageCore.cc
-@@ -22,6 +22,8 @@
- #include "system/AllOfOutput.h"
- #include "system/SharedMem.h"
- 
-+using std::ostringstream;
-+
- void PatcherCottageCore( basevector L, basevector R, const int sep,
-      const int dev, vecbasevector& reads, vecqualvector& quals,
-      vec< pair<int,int> >& pairs, String& report,      
---- allpathslg-52488/src/paths/PolymorphismRemoveCore.h
-+++ allpathslg-52488/src/paths/PolymorphismRemoveCore.h
-@@ -19,7 +19,7 @@
- 
- #include "kmers/naif_kmer/KmerFreqAffixesMap.h"
- 
--
-+using std::map;
- 
- typedef Kmer29                     Kmer_t;
- typedef KmerFreqAffixes<Kmer_t>    KmerRec_t;
---- allpathslg-52488/src/paths/ReadsToPathsCoreX.cc
-+++ allpathslg-52488/src/paths/ReadsToPathsCoreX.cc
-@@ -20,6 +20,8 @@
- #include "paths/MakeAlignsPathsParallelX.h"
- #include "paths/ReadsToPathsCoreX.h"
- 
-+using std::map;
-+
- static inline 
- String Tag(String S = "RTPCX") { return Date() + " (" + S + "): "; } 
- 
---- allpathslg-52488/src/paths/RemodelGapTools.cc
-+++ allpathslg-52488/src/paths/RemodelGapTools.cc
-@@ -18,6 +18,9 @@
- #include "paths/RemodelGapTools.h"
- #include "random/NormalDistribution.h"
- 
-+using std::istringstream;
-+using std::ostringstream;
-+
- // GapComp
- //
- // d = possible gap
---- allpathslg-52488/src/paths/reporting/CLinkBundle.cc
-+++ allpathslg-52488/src/paths/reporting/CLinkBundle.cc
-@@ -8,6 +8,8 @@
- 
- #include "paths/reporting/CLinkBundle.h"
- 
-+using std::make_pair;
-+
- /**
-  * CLinkBundle
-  * Constructor
---- allpathslg-52488/src/paths/reporting/CSuperLinks.cc
-+++ allpathslg-52488/src/paths/reporting/CSuperLinks.cc
-@@ -15,6 +15,8 @@
- #include "paths/reporting/COffset.h"
- #include "paths/reporting/CSuperLinks.h"
- 
-+using std::set;
-+
- /**
-  * class CSuperLinks
-  * Constructor
---- allpathslg-52488/src/paths/reporting/MapSeeds.cc
-+++ allpathslg-52488/src/paths/reporting/MapSeeds.cc
-@@ -24,7 +24,7 @@
- #include "paths/simulation/Placement.h"
- #include "feudal/BinaryStream.h"
- 
--
-+using std::ostringstream;
- 
- // MakeDepend: dependency QueryLookupTable
- 
---- allpathslg-52488/src/paths/SamplePairedReadDistributions.cc
-+++ allpathslg-52488/src/paths/SamplePairedReadDistributions.cc
-@@ -68,6 +68,8 @@
- #include "math/IntDistribution.h"
- #include "math/IntFrequencies.h"
- 
-+using std::list;
-+
- static inline 
- String Tag(String S = "SPRD") { return Date() + " (" + S + "): "; } 
- 
---- allpathslg-52488/src/paths/SamplePairedReadStats.cc
-+++ allpathslg-52488/src/paths/SamplePairedReadStats.cc
-@@ -46,6 +46,8 @@
- #include "paths/HyperBasevector.h"
- #include "paths/ReadsToPathsCoreX.h"
- 
-+using std::list;
-+
- // auxiliary routines    -------------------------------
- void pair_alignment_data( const PairsManager& pairs, const vecbasevector& reads, const VecQualNibbleVec &quals,
- 			  FirstLookupFinderECJ& lfinder, FirstLookupFilterECJ& lfilter,
---- allpathslg-52488/src/paths/SimpleGapCloser.cc
-+++ allpathslg-52488/src/paths/SimpleGapCloser.cc
-@@ -44,6 +44,8 @@
- #include "paths/Unipath.h"
- #include "system/AllOfOutput.h"
- 
-+using std::ostringstream;
-+
- class bridge {
- 
-      public:
---- allpathslg-52488/src/paths/SimpleWalk.cc
-+++ allpathslg-52488/src/paths/SimpleWalk.cc
-@@ -15,6 +15,9 @@
- #include "paths/PairedPair.h"
- #include "paths/SimpleWalk.h"
- 
-+using std::make_pair;
-+using std::priority_queue;
-+
- namespace
- {
- 
---- allpathslg-52488/src/paths/simulation/VCF.cc
-+++ allpathslg-52488/src/paths/simulation/VCF.cc
-@@ -16,6 +16,8 @@
- #include "system/Assert.h"
- #include <utility>
- 
-+using std::istringstream;
-+
- namespace {
- 
- // split - tokenize a string based on a separator and return a vector of strings representing the
---- allpathslg-52488/src/paths/simulation/VCF.h
-+++ allpathslg-52488/src/paths/simulation/VCF.h
-@@ -21,7 +21,8 @@
- 
- using std::string;
- using std::vector;
--
-+using std::ostringstream;
-+using std::map;
- 
- // VCFWriter use a streamlined data structure compared to VCF, which was hard coded to use VCFChromosome
- class VCFWriter
---- allpathslg-52488/src/paths/SubmissionPrep.cc
-+++ allpathslg-52488/src/paths/SubmissionPrep.cc
-@@ -21,6 +21,8 @@
- #include "paths/AssemblyCleanupTools.h"
- #include "math/HoInterval.h"
- 
-+using std::ostringstream;
-+
- /**
-  * SubmissionPrep
-  *
---- allpathslg-52488/src/paths/SubsumptionList.cc
-+++ allpathslg-52488/src/paths/SubsumptionList.cc
-@@ -2,6 +2,8 @@
- 
- #include "paths/SubsumptionList.h"
- 
-+using std::back_inserter;
-+
- // Functions to translate pathIds to indexes and back.
- 
- OrientedKmerPathId  PathIdFromIndex( int index ) 
---- allpathslg-52488/src/paths/SuperBaseVector.h
-+++ allpathslg-52488/src/paths/SuperBaseVector.h
-@@ -10,6 +10,8 @@
- #include <numeric>
- #include <functional>
- 
-+using std::mem_fun_ref;
-+
- /// A simple class which holds a series of basevectors with
- /// (possibly negative) gaps between them.  This is what a 
- /// KmerPath logically maps to in sequence space.  The function
---- allpathslg-52488/src/paths/UnibaseCopyNumber3.cc
-+++ allpathslg-52488/src/paths/UnibaseCopyNumber3.cc
-@@ -43,7 +43,7 @@
- #include <omp.h>
- // MakeDepend: library OMP
- 
--
-+using std::istrstream;
- 
- // Check if the gap size from u1 to u2 is the same as from u2* to u1*.
- void CheckGaps(
---- allpathslg-52488/src/paths/UnipathEval.cc
-+++ allpathslg-52488/src/paths/UnipathEval.cc
-@@ -35,6 +35,9 @@
- #include <omp.h>
- // MakeDepend: library OMP
- 
-+using std::ostringstream;
-+using std::list;
-+
- typedef double gc_t;
- typedef int unipath_size_t;
- typedef BinsVec2 < unipath_size_t, gc_t, PredictionStats > bin2PredStat;
---- allpathslg-52488/src/paths/UnipathFixerTools.cc
-+++ allpathslg-52488/src/paths/UnipathFixerTools.cc
-@@ -33,6 +33,8 @@
- #include "util/SearchFastb2Core.h"
- #include <vector>
- 
-+using std::ostringstream;
-+
- size_t const PCottageJoinData::HEADER;
- 
- void AlignReadsToUnipaths( const String& run_dir, const String& jump_reads,
---- allpathslg-52488/src/paths/UnipathNhoodCommon.cc
-+++ allpathslg-52488/src/paths/UnipathNhoodCommon.cc
-@@ -12,6 +12,8 @@
- #include "paths/simulation/Placement.h"
- #include <sstream>
- 
-+using std::ostringstream;
-+
- /**
-    Function: PrintNhood
- 
---- allpathslg-52488/src/paths/UnipathPatcher.cc
-+++ allpathslg-52488/src/paths/UnipathPatcher.cc
-@@ -47,6 +47,8 @@
- #include "paths/UnipathFixerTools.h"
- #include "system/SharedMem.h"
- 
-+using std::istrstream;
-+
- void GapStatsAlt( vec<int> gap, vec<int> gapdev, int& gap_ave, int& gapdev_ave )
- {
-      // If there are less than six gaps, we directly compute their mean.
---- allpathslg-52488/src/paths/Uniseq.cc
-+++ allpathslg-52488/src/paths/Uniseq.cc
-@@ -498,7 +498,7 @@
-           const gapster& gx = G( ).EdgeObjectByIndexFrom( x, 0 );
-           uniseq p = Vert(x);
-           int y = From(x)[0];
--          if ( !To(y).size( ) == 2 ) continue;
-+          if ( !(To(y).size( ) == 2) ) continue;
-           int e = -1;
-           for ( int j = 0; j < To(y).isize( ); j++ )
-                if ( To(y)[j] != x ) e = j;
-@@ -518,7 +518,7 @@
-           const gapster& gx = G( ).EdgeObjectByIndexTo( x, 0 );
-           uniseq p = Vert(x);
-           int y = To(x)[0];
--          if ( !From(y).size( ) == 2 ) continue;
-+          if ( !(From(y).size( ) == 2) ) continue;
-           int e = -1;
-           for ( int j = 0; j < From(y).isize( ); j++ )
-                if ( From(y)[j] != x ) e = j;
---- allpathslg-52488/src/paths/Useq.cc
-+++ allpathslg-52488/src/paths/Useq.cc
-@@ -10,6 +10,8 @@
- #include "CoreTools.h"
- #include "paths/Useq.h"
- 
-+using std::make_pair;
-+
- int useq::Kmers( ) const
- {    Assert( unibases_ != 0 );
-      int kmers = 0;
---- allpathslg-52488/src/PrintAlignment.h
-+++ allpathslg-52488/src/PrintAlignment.h
-@@ -14,6 +14,8 @@
- #include "CoreTools.h"
- #include "Qualvector.h"
- 
-+using std::ostringstream;
-+
- void PrintBlanks( ostream& out, int n );
- 
- template<class BASEVEC>
---- allpathslg-52488/src/Qualvector.cc
-+++ allpathslg-52488/src/Qualvector.cc
-@@ -10,6 +10,8 @@
- #include "FastIfstream.h"
- #include "Qualvector.h"
- 
-+using std::istrstream;
-+
- /// \file
- /// \ingroup grp_quals
- /// \copydoc Qualvector.h
---- allpathslg-52488/src/ReadLocation.cc
-+++ allpathslg-52488/src/ReadLocation.cc
-@@ -16,6 +16,9 @@
- #include "Vec.h"
- #include "system/file/FileReader.h"
- 
-+using std::streampos;
-+using std::map;
-+
- void read_location::ForceInBounds( ostream * out_ptr )
- {    if ( (int) LengthOfRead( ) > LengthOfContig( ) )
-      {    if ( out_ptr )
---- allpathslg-52488/src/ReadLocationUtil.cc
-+++ allpathslg-52488/src/ReadLocationUtil.cc
-@@ -9,7 +9,7 @@
- #include "STLExtensions.h"
- #include "VecAlignmentPlus.h"
- 
--
-+using std::map;
- 
- int AlignsCount( const vec<read_location> &locs,
- 		 int loc_id,
---- allpathslg-52488/src/reporting/ScaffoldLayout.cc
-+++ allpathslg-52488/src/reporting/ScaffoldLayout.cc
-@@ -21,6 +21,8 @@
- #include <omp.h>
- // MakeDepend: library OMP
- 
-+using std::ostringstream;
-+
- int main(int argc, char **argv)
- {
-      RunTime( );
---- allpathslg-52488/src/SeqInterval.cc
-+++ allpathslg-52488/src/SeqInterval.cc
-@@ -9,6 +9,7 @@
- #include "SeqInterval.h"
- #include "Vec.h"
- 
-+using std::min;
- 
- /*
-  * seq_interval
---- allpathslg-52488/src/SeqInterval.h
-+++ allpathslg-52488/src/SeqInterval.h
-@@ -14,7 +14,10 @@
- #include <algorithm>
- #include <iostream>
- 
--using namespace std;
-+using std::binary_function;
-+using std::ostream;
-+using std::istream;
-+using std::max;
- 
- /*
-  * class seq_interval
---- allpathslg-52488/src/Set.h
-+++ allpathslg-52488/src/Set.h
-@@ -16,6 +16,8 @@
- #include <iostream>
- #include <set>
- 
-+using std::set;
-+
- template <class T, class C=std::less<T>>
- using StdSet = std::set<T,C,typename DefaultAllocator<T>::type>;
- 
---- allpathslg-52488/src/ShortVector.h
-+++ allpathslg-52488/src/ShortVector.h
-@@ -14,6 +14,8 @@
- #include "system/Types.h"
- #include "feudal/BinaryStream.h"
- 
-+using std::uninitialized_fill_n;
-+
- // ================================================================================
- //
- // A shortvector holds a list of up to 255 things of any type T.  
---- allpathslg-52488/src/STLExtensions.h
-+++ allpathslg-52488/src/STLExtensions.h
-@@ -9,8 +9,6 @@
- #ifndef STLEXTENSIONS_H
- #define STLEXTENSIONS_H
- 
--using namespace std;
--
- #include <functional>
- #include <vector>
- #include <bitset>
-@@ -21,6 +19,14 @@
- #include "feudal/BinaryStream.h"
- #include "system/StaticAssert.h"
- 
-+using std::binary_function;
-+using std::unary_function;
-+using std::pair;
-+using std::bitset;
-+using std::initializer_list;
-+using std::vector;
-+using std::ostream;
-+
- /// minimum<T> is a function object.  
- ///
- /// If f is an object of class minimum<T> and x and y are objects of
---- allpathslg-52488/src/system/MiscUtil.cc
-+++ allpathslg-52488/src/system/MiscUtil.cc
-@@ -21,6 +21,8 @@
- #include "system/HTMLUtils.h"
- #include "system/Utils.h"
- 
-+using std::list;
-+
- static Bool makeOnlyIfNeeded = True;
- 
- void SetMakeOnlyIfNeeded( Bool newMakeOnlyIfNeeded ) {
---- allpathslg-52488/src/system/MiscUtil.h
-+++ allpathslg-52488/src/system/MiscUtil.h
-@@ -27,6 +27,9 @@
- #include "CommonSemanticTypes.h"
- #include "graph/Digraph.h"
- 
-+using std::map;
-+using std::set;
-+
- // Semantic type: shellcmd_t
- // The name of a shell command.
- SemanticType( String, shellcmd_t );
---- allpathslg-52488/src/system/ParsedArgs.cc
-+++ allpathslg-52488/src/system/ParsedArgs.cc
-@@ -26,6 +26,9 @@
- #include "system/HostName.h"
- #include "system/UseGDB.h"
- 
-+using std::istrstream;
-+using std::mem_fun_ref;
-+
- #ifndef FatalErr
-      #define FatalErr(message) { cout << message << endl << endl; exit(-1); }
- #endif
---- allpathslg-52488/src/system/ParsedArgs.h
-+++ allpathslg-52488/src/system/ParsedArgs.h
-@@ -97,6 +97,8 @@
- #include "TokenizeString.h"
- #include "ParseSet.h"
- 
-+using std::stringstream;
-+
- class parsed_arg_help {
- 
-  public:
---- allpathslg-52488/src/system/ProcBuf.cc
-+++ allpathslg-52488/src/system/ProcBuf.cc
-@@ -15,6 +15,8 @@
- #include <sys/wait.h>
- #include <unistd.h>
- 
-+using std::ios_base;
-+
- namespace
- {
- size_t const BUFFER_SIZE = 8192;
---- allpathslg-52488/src/system/RunTime.cc
-+++ allpathslg-52488/src/system/RunTime.cc
-@@ -41,6 +41,10 @@
-      #include <unwind.h>
- #endif
- 
-+using std::strstream;
-+using std::hex;
-+using std::setw;
-+
- /// ===========================================================================
- ///
- /// ReturnAddress(i), where 0 <= i <= 100: get the return address.  The
---- allpathslg-52488/src/system/RunTime.h
-+++ allpathslg-52488/src/system/RunTime.h
-@@ -14,6 +14,8 @@
- #include "system/Exit.h"
- #include "system/Types.h"
- 
-+using std::ostream;
-+
- typedef void ArachneSignalHandler(int, siginfo_t*, void*);
- 
- void arachne_signal_handler( int signal_number, siginfo_t* info, void* context,
---- allpathslg-52488/src/system/System.cc
-+++ allpathslg-52488/src/system/System.cc
-@@ -36,6 +36,10 @@
- 
- #include <dirent.h>
- 
-+using std::istringstream;
-+using std::istream_iterator;
-+using std::ostringstream;
-+
- int SystemInternal( String command, const char *shell,
-                         int* pStatus, int* pErrNo )
- {
-@@ -1088,7 +1092,7 @@
- 
- bool isReadable( String const& filename )
- {    ifstream ifs(filename.c_str());
--     return ifs;    }
-+     return static_cast<bool>(ifs);    }
- 
- int Glob( const String& x, vector<String>& xs )
- {    glob_t globbuf;
---- allpathslg-52488/src/system/System.h
-+++ allpathslg-52488/src/system/System.h
-@@ -21,6 +21,18 @@
- #include "system/Exit.h"
- #include "system/file/TempFile.h"
- 
-+using std::vector;
-+using std::ostream;
-+using std::ofstream;
-+using std::ifstream;
-+using std::istream;
-+using std::ios;
-+using std::cout;
-+using std::flush;
-+using std::endl;
-+using std::setprecision;
-+using std::fixed;
-+
- #ifndef InputErr
-      #define InputErr(message)                                \
-      cout << "\nFatal error at " << Date() << ": " << message \
---- allpathslg-52488/src/system/TraceVal.h
-+++ allpathslg-52488/src/system/TraceVal.h
-@@ -25,6 +25,9 @@
- #include "system/Assert.h"
- #include "system/Exit.h"
- 
-+using std::cout;
-+using std::endl;
-+
- // Macros: Tracing macros
- //   TRACEVAL_ON - undefine if you're not doing tracing
- //   TRACEVAL_STOP_TRACING_COPIES -- call before an operation that shuffles
---- allpathslg-52488/src/system/Types.h
-+++ allpathslg-52488/src/system/Types.h
-@@ -14,7 +14,7 @@
- #include <cstdlib>
- #include <netinet/in.h>
- 
--using namespace std;
-+
- 
- // This assumes that all suns run Solaris...
- #if __sun == 1
---- allpathslg-52488/src/system/WorklistUtils.cc
-+++ allpathslg-52488/src/system/WorklistUtils.cc
-@@ -32,6 +32,10 @@
- #include <sys/resource.h>
- #include <unistd.h>
- 
-+using std::istringstream;
-+using std::istream_iterator;
-+using std::min;
-+
- namespace
- {
-     pthread_t gMainThread;
---- allpathslg-52488/src/util/FastaParser.cc
-+++ allpathslg-52488/src/util/FastaParser.cc
-@@ -22,6 +22,7 @@
- 
- using std::string;
- using std::vector;
-+using std::istringstream;
- 
- char* FastaParser::readLine()
- {
---- allpathslg-52488/src/util/FastaParser.h
-+++ allpathslg-52488/src/util/FastaParser.h
-@@ -24,6 +24,8 @@
- #include <fstream>
- #include <vector>
- 
-+using std::max;
-+
- /// Base class for the parsers for sequence, quality, and bits which follow.
- class FastaParser
- {
---- allpathslg-52488/src/util/FastbStats.cc
-+++ allpathslg-52488/src/util/FastbStats.cc
-@@ -18,6 +18,8 @@
- 
- #include "random/Random.h"
- 
-+using std::map;
-+
- typedef VirtualMasterVec<BaseVec> VBaseVecVec;
- 
- 
---- allpathslg-52488/src/util/Happening.cc
-+++ allpathslg-52488/src/util/Happening.cc
-@@ -25,6 +25,8 @@
- #include "FastIfstream.h"
- #include "MainTools.h"
- 
-+using std::istringstream;
-+
- vec<String> tracebacks;
- Bool TALLYG;
- 
---- allpathslg-52488/src/util/MemMonitor.cc
-+++ allpathslg-52488/src/util/MemMonitor.cc
-@@ -21,7 +21,7 @@
- #include <signal.h>
- #include <time.h>
- 
--using namespace std;
-+using std::string;
- 
- // convertion factors between jiffies and seconds (check your system!!!)
- const double sec_jif = 100.0;
---- allpathslg-52488/src/util/Quala2Qualb.cc
-+++ allpathslg-52488/src/util/Quala2Qualb.cc
-@@ -11,6 +11,8 @@
- #include "FastIfstream.h"
- #include "Qualvector.h"
- 
-+using std::istrstream;
-+
- int main(int argc, char *argv[])
- {
-   RunTime();
---- allpathslg-52488/src/util/QualbStats.cc
-+++ allpathslg-52488/src/util/QualbStats.cc
-@@ -20,6 +20,7 @@
- #include "Qualvector.h"
- #include "Basevector.h"
- 
-+using std::scientific;
- 
- #define NQ 256
- 
---- allpathslg-52488/src/util/ReadTrack.cc
-+++ allpathslg-52488/src/util/ReadTrack.cc
-@@ -33,6 +33,9 @@
- #include "util/ReadTracker.h"
- #include "util/RunCommand.h"
- 
-+using std::map;
-+using std::set;
-+
- // Return filename portion of path (after last slash)
- String basename(const String path)
- {
---- allpathslg-52488/src/util/ReadTracker.cc
-+++ allpathslg-52488/src/util/ReadTracker.cc
-@@ -11,6 +11,9 @@
- #include "VecUtilities.h"
- #include "util/ReadTracker.h"
- 
-+using std::string;
-+using std::istringstream;
-+
- unsigned int 
- ReadTracker::AddSource(String s)
- {
---- allpathslg-52488/src/util/RunCommand.cc
-+++ allpathslg-52488/src/util/RunCommand.cc
-@@ -14,6 +14,8 @@
- #include <unistd.h>
- #include <sstream>
- 
-+using std::ostringstream;
-+
- /**
-  * RunCommand
-  */
---- allpathslg-52488/src/util/TextTable.cc
-+++ allpathslg-52488/src/util/TextTable.cc
-@@ -13,6 +13,8 @@
- #include <sstream>
- #include <iterator>
- 
-+using std::max;
-+
- vec<vec<String> > TextTable::GetTable( ) const {
-     vec<vec<String> > table;
-     for ( size_t i = 0; i < lines.size(); ++i ) {
---- allpathslg-52488/src/util/TextTable.h
-+++ allpathslg-52488/src/util/TextTable.h
-@@ -33,6 +33,8 @@
- #include "Vec.h"
- #include "feudal/TrackingAllocator.h"
- 
-+using std::string;
-+
- class TextTable {
- public:
-     // == Special types to draw line and manipulate tables ==
---- allpathslg-52488/src/Vec.h
-+++ allpathslg-52488/src/Vec.h
-@@ -50,6 +50,11 @@
- #include "Compare.h"
- #include "system/file/FileReader.h"
- 
-+using std::numeric_limits;
-+using std::ostream_iterator;
-+using std::setfill;
-+using std::setw;
-+
- /////////////////////////////////////////////////////////////////////////////
- //
- //  vec Class Declaration and Template Definitions
---- allpathslg-52488/src/VecOverlap.cc
-+++ allpathslg-52488/src/VecOverlap.cc
-@@ -12,6 +12,9 @@
- #include "STLExtensions.h"
- #include <numeric>
- 
-+using std::max;
-+using std::make_pair;
-+
- // Represents the suffix of the index'th word starting at the pos'th
- // character.
- template <class T>
---- allpathslg-52488/src/VecUtilities.h
-+++ allpathslg-52488/src/VecUtilities.h
-@@ -37,6 +37,9 @@
- #include "Vec.h"
- #include <cstddef>
- 
-+using std::less;
-+using std::equal_to;
-+using std::greater;
- 
- /////////////////////////////////////////////////////////////////////////////
- //
diff --git a/sci-biology/bedtools/Manifest b/sci-biology/bedtools/Manifest
index dcb1662a4644..68f58e97b0bc 100644
--- a/sci-biology/bedtools/Manifest
+++ b/sci-biology/bedtools/Manifest
@@ -1,4 +1,4 @@
-AUX bedtools-2.26.0-fix-buildsystem.patch 26994 BLAKE2B 971281e6cfc317729a3a294822d52a2c897988230a538eff0e368676c7518bf4f91dafdd412acb29bab5fccfa564c04c733567e27a4c5e3435c3bf95b0819096 SHA512 16b4994a9e3bad0a17f0be94fe9412c6c8aee2b5d909007c655fcf3de60c221d3f9ddbe558df7e54466481910d5fa9b871b8123d9bdb1e7c695682990d2457f4
-DIST bedtools-2.26.0.tar.gz 19939711 SHA256 65f32f32cbf1b91ba42854b40c604aa6a16c7d3b3ec110d6acf438eb22df0a4a SHA512 b224adcc09322e90ef389e8172e14572b68f164185fe1a8814db1c47bb4f15656ca8c0ff0061017eb54d76affbe0d0f5793d893b8ab489b56eaf0818616a5def WHIRLPOOL 8d6e3b58dc38d7ab91482ffe5ee773953864ca79bdbf005b17fec51952a869b39bf775d836ed34496a7784565bb84380eef284e285e842d52229fe2fc6a214b2
-EBUILD bedtools-2.26.0.ebuild 870 BLAKE2B 99ec3ce092c728e9c71b6801ee8eba9fbe0dcd003e9a62058111bf33171fe5d34003f33cfd260a1b8890f36198e0d62e9d71a5cd41d6e9e91264332cc77c2535 SHA512 e6b4a079ac25c4d397b4377d5adad5ffa66e690c20d33c5ed7bc2eaf72f00235395232b574ab266ae4373ede77296e067f41436303ff4e4836e67eca7a3514fb
+DIST bedtools-2.26.0-fix-buildsystem.patch.bz2 2584 BLAKE2B 550cd03a0c01217adb347587cb75bdc2ffa4e03ad6ad66535b22d423e6f030e237b0ccfd3d1bd3e434cb9cc2a007971517f03e9ceabc08b63c725bac786e23e8 SHA512 0a7835f560102ce6183736faea6a2be05609b69bb8efdaf98b9d7057e24aa1ebe9d6067118b95c76470ca341b151970db532094ee70ca333075aed7c47509ba3
+DIST bedtools-2.26.0.tar.gz 19939711 BLAKE2B 8f6ee6ed755c638dbdd0a4750a5348c28a865f36eaafef6160e90f62912cb0a6b719713935ba68dad74bc591e3f37db49eab54a06a316dc00e4ec82a5dca71dc SHA512 b224adcc09322e90ef389e8172e14572b68f164185fe1a8814db1c47bb4f15656ca8c0ff0061017eb54d76affbe0d0f5793d893b8ab489b56eaf0818616a5def
+EBUILD bedtools-2.26.0.ebuild 945 BLAKE2B f6eef93634c2da37b0a070e11e49db2c4efea4339677f52dd4787f04989d739e96a731fd4d737802cc0c6161a4bf1390b4509762e2cb33e677f4700c1648e311 SHA512 f4c841281eb85613bf9fdd4db9f6f9d1dccf24e5fe72d99a7e72940a52e346aed319fd92b6750ca489630f6a25c395680507492fdd5c42b6ba54a68aff0432d3
 MISC metadata.xml 761 BLAKE2B 35d57919e32a4b8bd6070ab5a513f62578394d43098d9e7b9b0765fd57d684c049dad9ec1b315044518bf01535d505e9d9d3fee540308df40c0b70886db8e49f SHA512 2d98b9559ef00bee2b741f9e7d22645442ba161f3cadb32c6366b39fcd71b6eac52afd210f59ae709a15cba36a2d0a47341345740e0cab6a1f6bfdffed064770
diff --git a/sci-biology/bedtools/bedtools-2.26.0.ebuild b/sci-biology/bedtools/bedtools-2.26.0.ebuild
index eeedf606debe..0520143f3d9a 100644
--- a/sci-biology/bedtools/bedtools-2.26.0.ebuild
+++ b/sci-biology/bedtools/bedtools-2.26.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -9,7 +9,8 @@ inherit flag-o-matic python-any-r1 toolchain-funcs
 
 DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats"
 HOMEPAGE="https://bedtools.readthedocs.io/"
-SRC_URI="https://github.com/arq5x/${PN}2/releases/download/v${PV}/${P}.tar.gz"
+SRC_URI="https://github.com/arq5x/${PN}2/releases/download/v${PV}/${P}.tar.gz
+	https://dev.gentoo.org/~mgorny/dist/${PN}-2.26.0-fix-buildsystem.patch.bz2"
 
 LICENSE="GPL-2"
 SLOT="0"
@@ -26,7 +27,7 @@ RDEPEND="sys-libs/zlib"
 S="${WORKDIR}/${PN}2"
 
 DOCS=( README.md RELEASE_HISTORY )
-PATCHES=( "${FILESDIR}/${PN}-2.26.0-fix-buildsystem.patch" )
+PATCHES=( "${WORKDIR}/${PN}-2.26.0-fix-buildsystem.patch" )
 
 src_configure() {
 	append-lfs-flags
diff --git a/sci-biology/bedtools/files/bedtools-2.26.0-fix-buildsystem.patch b/sci-biology/bedtools/files/bedtools-2.26.0-fix-buildsystem.patch
deleted file mode 100644
index fb6be18d7071..000000000000
--- a/sci-biology/bedtools/files/bedtools-2.26.0-fix-buildsystem.patch
+++ /dev/null
@@ -1,869 +0,0 @@
-* Make build system verbose (https://bugs.gentoo.org/show_bug.cgi?id=429308)
-* Remove CXX and CXXFLAGS, ebuild sets them
-* Handle python via Gentoo's EPYTHON instead
-
---- a/Makefile
-+++ b/Makefile
-@@ -16,17 +16,9 @@
- export BIN_DIR	= bin
- export SRC_DIR	= src
- export UTIL_DIR	= src/utils
--export CXX		= g++
--ifeq ($(DEBUG),1)
--export CXXFLAGS = -Wall -O0 -g -fno-inline -fkeep-inline-functions -D_FILE_OFFSET_BITS=64 -fPIC -DDEBUG -D_DEBUG
--else
--export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
--endif
- export LIBS		= -lz
- export BT_ROOT  = src/utils/BamTools/
- 
--prefix ?= /usr/local
--
- SUBDIRS = $(SRC_DIR)/annotateBed \
- 		  $(SRC_DIR)/bamToBed \
- 		  $(SRC_DIR)/bamToFastq \
-@@ -135,13 +127,13 @@
- 
- all: print_banner $(OBJ_DIR) $(BIN_DIR) autoversion $(UTIL_SUBDIRS) $(SUBDIRS)
- 	@echo "- Building main bedtools binary."
--	@$(CXX) $(CXXFLAGS) $(CPPFLAGS) -c src/bedtools.cpp -o obj/bedtools.o $(INCLUDES)
--	@$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS) $(LDFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c src/bedtools.cpp -o obj/bedtools.o $(INCLUDES)
-+	$(CXX) $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS)
- 	@echo "done."
- 
- 	@echo "- Creating executables for old CLI."
--	@python scripts/makeBashScripts.py
--	@chmod +x bin/*
-+	$(EPYTHON) scripts/makeBashScripts.py
-+	chmod +x bin/*
- 	@echo "done."
- 
- 
---- a/src/annotateBed/Makefile
-+++ b/src/annotateBed/Makefile
-@@ -26,7 +26,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- 		
- clean:
---- a/src/bamToBed/Makefile
-+++ b/src/bamToBed/Makefile
-@@ -28,7 +28,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) 
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)  -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/bamToFastq/Makefile
-+++ b/src/bamToFastq/Makefile
-@@ -24,7 +24,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) 
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/bed12ToBed6/Makefile
-+++ b/src/bed12ToBed6/Makefile
-@@ -27,7 +27,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/bedpeToBam/Makefile
-+++ b/src/bedpeToBam/Makefile
-@@ -33,7 +33,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- $(EXT_OBJECTS):
- 	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools/	
---- a/src/bedToBam/Makefile
-+++ b/src/bedToBam/Makefile
-@@ -30,7 +30,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/bedToIgv/Makefile
-+++ b/src/bedToIgv/Makefile
-@@ -28,7 +28,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/closestFile/Makefile
-+++ b/src/closestFile/Makefile
-@@ -40,7 +40,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/clusterBed/Makefile
-+++ b/src/clusterBed/Makefile
-@@ -25,7 +25,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/complementFile/Makefile
-+++ b/src/complementFile/Makefile
-@@ -42,7 +42,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 	
- clean:
- 	@echo "Cleaning up."
---- a/src/coverageFile/Makefile
-+++ b/src/coverageFile/Makefile
-@@ -38,7 +38,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/expand/Makefile
-+++ b/src/expand/Makefile
-@@ -27,7 +27,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 	
- clean:
- 	@echo "Cleaning up."
---- a/src/fastaFromBed/Makefile
-+++ b/src/fastaFromBed/Makefile
-@@ -30,7 +30,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/fisher/Makefile
-+++ b/src/fisher/Makefile
-@@ -51,7 +51,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 	
- clean:
- 	@echo "Cleaning up."
---- a/src/flankBed/Makefile
-+++ b/src/flankBed/Makefile
-@@ -26,7 +26,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 		
- clean:
- 	@echo "Cleaning up."
---- a/src/genomeCoverageBed/Makefile
-+++ b/src/genomeCoverageBed/Makefile
-@@ -27,7 +27,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/getOverlap/Makefile
-+++ b/src/getOverlap/Makefile
-@@ -26,7 +26,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- 	
- clean:
---- a/src/groupBy/Makefile
-+++ b/src/groupBy/Makefile
-@@ -42,7 +42,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 	
- clean:
- 	@echo "Cleaning up."
---- a/src/intersectFile/Makefile
-+++ b/src/intersectFile/Makefile
-@@ -39,7 +39,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 	
- clean:
- 	@echo "Cleaning up."
---- a/src/jaccard/Makefile
-+++ b/src/jaccard/Makefile
-@@ -43,7 +43,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 	
- clean:
- 	@echo "Cleaning up."
---- a/src/linksBed/Makefile
-+++ b/src/linksBed/Makefile
-@@ -25,7 +25,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/mapFile/Makefile
-+++ b/src/mapFile/Makefile
-@@ -38,7 +38,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/maskFastaFromBed/Makefile
-+++ b/src/maskFastaFromBed/Makefile
-@@ -25,7 +25,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/mergeFile/Makefile
-+++ b/src/mergeFile/Makefile
-@@ -40,7 +40,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/multiBamCov/Makefile
-+++ b/src/multiBamCov/Makefile
-@@ -26,7 +26,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/multiIntersectBed/Makefile
-+++ b/src/multiIntersectBed/Makefile
-@@ -27,7 +27,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/nekSandbox1/Makefile
-+++ b/src/nekSandbox1/Makefile
-@@ -35,7 +35,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 	
- clean:
- 	@echo "Cleaning up."
---- a/src/nucBed/Makefile
-+++ b/src/nucBed/Makefile
-@@ -27,7 +27,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/pairToBed/Makefile
-+++ b/src/pairToBed/Makefile
-@@ -27,7 +27,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/pairToPair/Makefile
-+++ b/src/pairToPair/Makefile
-@@ -27,7 +27,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- 
- clean:
---- a/src/randomBed/Makefile
-+++ b/src/randomBed/Makefile
-@@ -23,7 +23,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/regressTest/Makefile
-+++ b/src/regressTest/Makefile
-@@ -24,24 +24,18 @@
- # ----------------------------------
- # define our source and object files
- # ----------------------------------
--#SOURCES= regressTestMain.cpp RegressTest.cpp RegressTest.h
--#OBJECTS= regressTestMain.o RegressTest.o
--#BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
-+SOURCES= regressTestMain.cpp RegressTest.cpp RegressTest.h
-+OBJECTS= regressTestMain.o RegressTest.o
-+BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
- PROGRAM= regressTest
- 
--
--all: #$(BUILT_OBJECTS)
--	@echo "compiling RegressTest.cpp"
--	@$(CXX) -c -o $(OBJ_DIR)/RegressTest.o RegressTest.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
--	@echo "compiling regressTestMain.cpp"
--	@$(CXX) -c -o $(OBJ_DIR)/regressTestMain.o regressTestMain.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+all: $(BUILT_OBJECTS)
- 	
- .PHONY: all
- 
--#$(BUILT_OBJECTS): $(SOURCES)
--#	@echo "  * compiling" $(*F).cpp
--#	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
--
-+$(BUILT_OBJECTS): $(SOURCES)
-+	@echo "  * compiling" $(*F).cpp
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/reldist/Makefile
-+++ b/src/reldist/Makefile
-@@ -30,7 +30,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 	
- clean:
- 	@echo "Cleaning up."
---- a/src/sampleFile/Makefile
-+++ b/src/sampleFile/Makefile
-@@ -37,7 +37,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 	
- clean:
- 	@echo "Cleaning up."
---- a/src/shiftBed/Makefile
-+++ b/src/shiftBed/Makefile
-@@ -26,7 +26,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/shuffleBed/Makefile
-+++ b/src/shuffleBed/Makefile
-@@ -28,7 +28,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/slopBed/Makefile
-+++ b/src/slopBed/Makefile
-@@ -26,7 +26,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/sortBed/Makefile
-+++ b/src/sortBed/Makefile
-@@ -26,7 +26,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/spacingFile/Makefile
-+++ b/src/spacingFile/Makefile
-@@ -37,7 +37,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 	
- clean:
- 	@echo "Cleaning up."
---- a/src/split/Makefile
-+++ b/src/split/Makefile
-@@ -25,7 +25,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/subtractFile/Makefile
-+++ b/src/subtractFile/Makefile
-@@ -40,7 +40,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 	
- clean:
- 	@echo "Cleaning up."
---- a/src/tagBam/Makefile
-+++ b/src/tagBam/Makefile
-@@ -28,7 +28,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/unionBedGraphs/Makefile
-+++ b/src/unionBedGraphs/Makefile
-@@ -27,7 +27,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/utils/BamTools/Makefile
-+++ b/src/utils/BamTools/Makefile
-@@ -56,12 +56,12 @@
- 
- $(LIBRARY): $(OBJECTS)
- 	@echo " * linking $(LIBRARY)"
--	ar cr $@ $^
-+	$(AR) cr $@ $^
- 	-ranlib $@
- 
- $(OBJECTS): $(SOURCES)
- 	@echo " * compiling" $(*F).cpp
--	@$(CXX) -c $(*D)/$(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -o $(*D)/$(*F).o
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -o $(*D)/$(*F).o -c $(*D)/$(*F).cpp
- 
- .PHONY: api
- api:
---- a/src/utils/BamTools-Ancillary/Makefile
-+++ b/src/utils/BamTools-Ancillary/Makefile
-@@ -21,7 +21,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/utils/bedFile/Makefile
-+++ b/src/utils/bedFile/Makefile
-@@ -20,7 +20,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- $(EXT_OBJECTS):
- 	@$(MAKE) --no-print-directory -C -W $(INCLUDES)
---- a/src/utils/bedFilePE/Makefile
-+++ b/src/utils/bedFilePE/Makefile
-@@ -17,7 +17,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- $(EXT_OBJECTS):
- 	@$(MAKE) --no-print-directory -C $(INCLUDES)
---- a/src/utils/bedGraphFile/Makefile
-+++ b/src/utils/bedGraphFile/Makefile
-@@ -19,7 +19,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- $(EXT_OBJECTS):
- 	@$(MAKE) --no-print-directory -C -W $(INCLUDES)
---- a/src/utils/BinTree/Makefile
-+++ b/src/utils/BinTree/Makefile
-@@ -28,7 +28,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- $(EXT_OBJECTS):
- 	@$(MAKE) --no-print-directory -C $(INCLUDES)
---- a/src/utils/BlockedIntervals/Makefile
-+++ b/src/utils/BlockedIntervals/Makefile
-@@ -23,7 +23,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib -c -o $@ $(*F).cpp
- 
- $(EXT_OBJECTS):
- 	@$(MAKE) --no-print-directory -C $(INCLUDES)
---- a/src/utils/chromsweep/Makefile
-+++ b/src/utils/chromsweep/Makefile
-@@ -20,7 +20,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- $(EXT_OBJECTS):
- 	@$(MAKE) --no-print-directory -C $(INCLUDES)
---- a/src/utils/Contexts/Makefile
-+++ b/src/utils/Contexts/Makefile
-@@ -36,7 +36,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/utils/driver/Makefile
-+++ b/src/utils/driver/Makefile
-@@ -85,7 +85,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 	
- clean:
- 	@echo "Cleaning up."
---- a/src/utils/Fasta/Makefile
-+++ b/src/utils/Fasta/Makefile
-@@ -19,7 +19,7 @@
- 	
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/utils/FileRecordTools/FileReaders/Makefile
-+++ b/src/utils/FileRecordTools/FileReaders/Makefile
-@@ -32,7 +32,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/utils/FileRecordTools/FileReaders/Makefile~
-+++ b/src/utils/FileRecordTools/FileReaders/Makefile~
-@@ -31,7 +31,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/utils/FileRecordTools/Makefile
-+++ b/src/utils/FileRecordTools/Makefile
-@@ -34,9 +34,9 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling FileRecordMgr.cpp"
--	@$(CXX) -c -o $(OBJ_DIR)/FileRecordMgr.o FileRecordMgr.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $(OBJ_DIR)/FileRecordMgr.o FileRecordMgr.cpp
- 	@echo "  * compiling FileRecordMergeMgr.cpp"
--	@$(CXX) -c -o $(OBJ_DIR)/FileRecordMergeMgr.o FileRecordMergeMgr.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $(OBJ_DIR)/FileRecordMergeMgr.o FileRecordMergeMgr.cpp
- 	
- 	
- 
---- a/src/utils/FileRecordTools/Records/Makefile
-+++ b/src/utils/FileRecordTools/Records/Makefile
-@@ -37,7 +37,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/utils/fileType/Makefile
-+++ b/src/utils/fileType/Makefile
-@@ -22,7 +22,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/utils/general/Makefile
-+++ b/src/utils/general/Makefile
-@@ -21,7 +21,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/utils/GenomeFile/Makefile
-+++ b/src/utils/GenomeFile/Makefile
-@@ -20,9 +20,9 @@
- 
- $(BUILT_OBJECTS): $(SOURCES) $(SUBDIRS)
- 	@echo "  * compiling GenomeFile.cpp"
--	@$(CXX) -c -o $(OBJ_DIR)/GenomeFile.o GenomeFile.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $(OBJ_DIR)/GenomeFile.o GenomeFile.cpp
- 	@echo "  * compiling NewGenomeFile.cpp"
--	@$(CXX) -c -o $(OBJ_DIR)/NewGenomeFile.o NewGenomeFile.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $(OBJ_DIR)/NewGenomeFile.o NewGenomeFile.cpp
- 
- #$(EXT_OBJECTS):
- #	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
---- a/src/utils/gzstream/Makefile
-+++ b/src/utils/gzstream/Makefile
-@@ -38,7 +38,7 @@
- UTILITIES_DIR = ../../utils/
- 	
- ${OBJ_DIR}/gzstream.o : gzstream.C gzstream.h
--	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -c -o $(OBJ_DIR)/gzstream.o gzstream.C $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $(OBJ_DIR)/gzstream.o gzstream.C
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/utils/KeyListOps/Makefile
-+++ b/src/utils/KeyListOps/Makefile
-@@ -31,7 +31,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- 
- $(EXT_OBJECTS):
---- a/src/utils/NewChromsweep/Makefile
-+++ b/src/utils/NewChromsweep/Makefile
-@@ -34,7 +34,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/utils/RecordOutputMgr/Makefile
-+++ b/src/utils/RecordOutputMgr/Makefile
-@@ -29,7 +29,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- $(EXT_OBJECTS):
- 	@$(MAKE) --no-print-directory -C $(INCLUDES)
---- a/src/utils/sequenceUtilities/Makefile
-+++ b/src/utils/sequenceUtilities/Makefile
-@@ -17,7 +17,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- $(EXT_OBJECTS):
- 	@$(MAKE) --no-print-directory -C $(INCLUDES)
---- a/src/utils/tabFile/Makefile
-+++ b/src/utils/tabFile/Makefile
-@@ -19,7 +19,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- $(EXT_OBJECTS):
- 	@$(MAKE) --no-print-directory -C -W $(INCLUDES)
---- a/src/utils/ToolBase/Makefile
-+++ b/src/utils/ToolBase/Makefile
-@@ -30,7 +30,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- $(EXT_OBJECTS):
- 	@$(MAKE) --no-print-directory -C $(INCLUDES)
---- a/src/utils/VectorOps/Makefile
-+++ b/src/utils/VectorOps/Makefile
-@@ -11,7 +11,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/utils/version/Makefile
-+++ b/src/utils/version/Makefile
-@@ -20,7 +20,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES) $(HEADERS)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/windowBed/Makefile
-+++ b/src/windowBed/Makefile
-@@ -27,7 +27,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/src/windowMaker/Makefile
-+++ b/src/windowMaker/Makefile
-@@ -26,7 +26,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- $(EXT_OBJECTS):
- 	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/genomeFile/
diff --git a/sci-biology/goby-cpp/Manifest b/sci-biology/goby-cpp/Manifest
index a0cf57197f35..c38de79d4ffa 100644
--- a/sci-biology/goby-cpp/Manifest
+++ b/sci-biology/goby-cpp/Manifest
@@ -1,10 +1,8 @@
-AUX Alignments.proto 26192 BLAKE2B 412eb735feb2e1a9b85f4b9ee24620052648f292f041968a2d7bfae52c124697a40813467c038da44b18a89c2e9dc554bf93c414553bd1397829205af2f0f632 SHA512 c5b67577bfd8432e64489dfb08333adcece8712a398497facb284b52c5b773eff79d71c6dc5bcb72ab21b977423530e27cac3fa2a888c3a00cca1a09faf1b00f
-AUX Reads.proto 3128 BLAKE2B 38af9aa9ac3e792791ee90a2506419dd2356618200c16924929796160c98b4cb5b2ca8ecb2b66085605b86227dc04f155f1c6610c07577ec0fbb3bde69da2384 SHA512 eed972f7f054096ba0e4b215e1551b8acdee6024cec6091abe2b92e268b09fb77d2e9c2a90520611da3bfe37e69a8341e406c4eccb57b0c88f3664f7f2818e27
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diff --git a/sci-biology/goby-cpp/files/Alignments.proto b/sci-biology/goby-cpp/files/Alignments.proto
deleted file mode 100644
index fe7f56647644..000000000000
--- a/sci-biology/goby-cpp/files/Alignments.proto
+++ /dev/null
@@ -1,597 +0,0 @@
-package goby;
-
-option java_package = "edu.cornell.med.icb.goby.alignments";
-
-option optimize_for = SPEED;
-
-/*
-  This message is written to 'basename'.entries as a very large chunked collection.
-*/
-message AlignmentCollection {
-    repeated AlignmentEntry alignment_entries = 1;
-}
-
-
-message AlignmentEntry {
-    /* Multiplicity of this entry. The number of times this  alignment entry would be repeated exactly the same if
-     query redundancy had not been removed by read factorization.
-    */
-    optional uint32 multiplicity = 7;
-
-    /*
-      Compressed stream of data. Removed since Goby 2.0 supports chunk codecs. Do not reuse field index 23
-      optional bytes compressed_data = 23;
-    */
-
-    /* An integer that uniquely identifies the query (a short read) in a set of alignment runs. When several
-      alignment runs are made with the same set of query sequences, equality of query index means that the query
-      sequences were the same. (Comparing integers for equality is much faster than comparing strings.)
-      This field is required (enforced by semantic validation in Goby 2.0+).
-    */
-    optional uint32 query_index = 1;
-    /* An integer that uniquely identifies the target (e.g., a chromosome) in a set of alignment runs. When several
-      alignment runs are made with the same set of target sequences, equality of target index means that the target
-      sequence was the same across the runs. (Comparing integers for equality is much faster than comparing strings.)
-      This field is required (enforced by semantic validation in Goby 2.0+).
-    */
-    optional uint32 target_index = 2;
-    /*
-     The position on the target of the start of the alignment between the query and the target.
-     In the following example, position is 3 because the third base of the query 'C' was aligned with
-     position 3 of the reference (two read bases were soft clipped: "ct"). This example shows that the
-     alignment can start at a mismatch if it was so constructed by the aligner.
-
-     0123456789
-     AAAAGTCAAA  target
-      ctCGTC     query
-    This field is required (enforced by semantic validation in Goby 2.0+).
-   */
-    optional uint32 position = 3;
-
-    /*
-       True when the query matches the target on the reverse strand
-    */
-    optional bool matching_reverse_strand = 6;
-
-    /*
-     The position on the query where the alignment starts. This value is different from zero
-     when some bases/residues of the query could not be aligned with the target.
-     TODO: Rename this to left_trim. Add a right_trim property.
-    */
-    optional uint32 query_position = 5;
-
-    /*
-     The score of the alignment, where larger scores indicate better matches between the query and the target.
-     If an aligner outputs only the number of mismatches between query and target, the score is taken to be
-     -(#mismatches(query,target)).
-    */
-    optional float score = 4;
-
-    /*
-      Number of bases/residues that differ in the alignment between query and target sequences.
-    */
-    optional uint32 number_of_mismatches = 8;
-
-    /*
-     Cumulative number of insertions and/or deletions present in the alignment.
-    */
-    optional uint32 number_of_indels = 9;
-
-    /*
-     Number of bases that have been aligned for the query. Please note that query_aligned_length must be
-     less or equal to query_length.
-    */
-    optional uint32 query_aligned_length = 11;
-
-    /*
-     Number of bases that have been aligned for the target.
-    */
-    optional uint32 target_aligned_length = 12;
-
-    repeated SequenceVariation sequence_variations = 13;
-
-    /*
-     Length of the query sequence.
-    */
-    optional uint32 query_length = 10;
-    /*
-      Mapping Quality (phred-scaled posterior probability that the mapping
-      position of this read is incorrect). Please note that different aligners
-      may estimate mapping quality with different approaches, resulting in aligner
-      specific differences in the distribution of mapping quality. It is recommended
-      to condition mapping quality on the aligner that produced the specific alignment
-      being processed. See aligner name and version in the header.
-      Note that the following description is preliminary. A clear specification is
-      needed:
-      The mapping quality should be proportional to the
-      log of the probability that the given mapping is the "correct" one.
-      So if there are five equally good mappings of a read to the genome,
-      the probability of each would be 0.2, and the mapping quality would be
-      something like -10*log10(1-0.2) = 1.  If a mapping is highly likely,
-      say a 1e-4 of it being wrong, then the mapping quality would be
-      -10*log10(1e-4) = 40.
-    */
-    optional int32 mapping_quality = 14;
-
-    /*
-       If this read was aligned with a pair, the flags for the pair alignment (based on SAM):
-          000000001    paired
-          000000010    properly paired
-          000000100    read unmapped
-          000001000    mate unmapped
-          000010000    read reverse strand
-          000100000    mate reverse strand
-          001000000    first in pair
-          010000000    second in pair
-          100000000    not primary alignment
-    */
-    optional uint32 pair_flags = 15;
-
-    /*
-     If there is an alignment entry for the paired read (the paired read was mapped), a link to the entry is given.
-    */
-    optional RelatedAlignmentEntry pair_alignment_link = 16;
-
-    /* Index of the read fragment from which this alignment was obtained. */
-    optional uint32 fragment_index = 17;
-
-    /* If a read spans exon-exon junctions some aligners (e.g., GSNAP) will output two or more
-      alignment entries, one for each matching part of the read, and link these entries with
-      spliced_alignment_links. The field spliced_forward_alignment_link points to the next
-      AlignmentEntry in the chain of spliced alignments.
-    */
-    optional RelatedAlignmentEntry spliced_forward_alignment_link = 18;
-
-    /* If a read spans exon-exon junctions some aligners (e.g., GSNAP) will output two or more
-      alignment entries, one for each matching part of the read, and link these entries with
-      spliced_alignment_links. The field spliced_backward_alignment_link points to the previous
-      AlignmentEntry in the chain of spliced alignments.
-    */
-    optional RelatedAlignmentEntry spliced_backward_alignment_link = 22;
-
-    /*
-      If a read spans exon-exon junctions some aligners (e.g., GSNAP) will output two alignment entries, one for each
-      matching part of the read, and flag describes the spliced_alignment_link with these
-      binary flags:
-        000000001    normal
-        000000010    novel
-    */
-    optional uint32 spliced_flags = 19;
-
-    /* The size of the insert used when making the sequence library. This is the total size of the DNA
-    fragment to sequence, without the adapters. This is not the length of sequence that separates the reads.
-    See http://seqanswers.com/forums/showthread.php?t=8730 for details. Insert size is inferred for each pair
-    of reads by the aligner and is recorded here if was estimated (i.e., for paired-end reads).
-    */
-    optional sint32 insert_size = 20;
-
-    /*
-       The sample index. Uniquely identifies the aligned sample this read was read from. Storing the sample index in the
-       alignment entry makes it possible to concat alignments from different origins and track what sample originally
-       contained each entry.
-    */
-    optional uint32 sample_index = 21;
-    /*
-        The total number of times the query index associated with this entry occurs across the entire alignment file.
-
-        This field is used to purge queryIndex->smallIndex associations after all instances of a queryindex have
-        been seen (see QueryIndexPermutation class). When each entry has a value for this field, the header field
-        query_index_occurrences is true.
-        This field is required (enforced by semantic validation in Goby 2.0+).
-    */
-    optional uint32 query_index_occurrences = 25;
-    /*
-        The total number of times the read matches the reference across the entire alignment file. This differs from
-        query_index_occurrences because reads that are matching through splice and pair links count as one for ambiguity.
-        The field can be used to filter by ambiguity-threshold on the fly after an alignment has been done (to restrict
-        entries to more smaller thresholds). When each entry has a value for this field, the header field
-        ambiguity_stored_in_entries is true.
-
-        This field is required (enforced by semantic validation in Goby 2.0+).
-    */
-    optional uint32 ambiguity = 27;
-    /*
-        List of BAM attributes, if the alignment was imported from BAM. The attributes are stored in exactly the format
-        allowed for BAM. For instance, X0:i:9  X1:i:1  MD:Z:68 RG:Z:SRR084825 will be stored as four strings:
-        "X0:i:9", "X1:i:1", "MD:Z:68", "RG:Z:SRR084825". Note that sam-to-compact will interpret some BAM attributes
-        and populate goby native fields. Such tags do not appear in bam_attributes, and are instead re-generated from
-        the corresponding goby native fields.
-        Since Goby 2.0.
-    */
-    repeated string bam_attributes = 50;
-    /*
-        Quality scores for all bases of the read.
-        Since Goby 2.0.
-    */
-    optional bytes read_quality_scores = 55;
-
-    /*
-        Origin index. An integer that references a ReadOriginInfo message in the alignment header and
-        makes it possible to track the origin of the read (especially useful after several alignments
-        have been merged/concatenated).
-        (Since Goby 2.0).
-    */
-    optional uint32 read_origin_index = 26;
-    /*
-    Bases that an aligner considered do not belong to the alignment of the read to the reference. Potentially
-    erroneous bases, or bases that belong to a different part of the reference genome. Left clipped bases are
-    stored in this field as character bases, or as an equal sign character '=' when the clipped base did match
-    the reference base. For instance "A=G" for three soft-clipped bases, the middle one matching the genome at
-    this position. The number of bases in softClippedBasesLeft is exactly equal to queryPosition.
-    */
-    optional string softClippedBasesLeft = 30;
-    /*
-    Bases that an aligner considered do not belong to the alignment of the read to the reference. Potentially
-    erroneous bases, or bases that belong to a different part of the reference genome. Right clipped bases are
-    stored in this field as character bases, or as an equal sign character '=' when the clipped base did match
-    the reference base. The number of bases in softClippedBasesRight is exactly equal
-    to  queryLength - queryAlignedLength - queryPosition.
-    */
-    optional string softClippedBasesRight = 31;
-
-    /*
-    Quality scores for bases in softClippedBasesLeft.  Stored in Phred Units.
-    */
-    optional bytes softClippedQualityLeft = 32;
-   /*
-    Quality scores for bases in softClippedBasesRight.  Stored in Phred Units.
-    */
-    optional bytes softClippedQualityRight = 33;
-    /*
-     Sequence for a read placed near this entry, but unmapped to the reference sequence. For instance, used to record
-     the sequence of a mate that did not map to the reference. We know that the mate maps in the proximity of this entry
-     (it is placed) but are unable to map it to a specific genomic position. The sequence is always given as obtained
-     from the reads file.
-    */
-    optional string placedUnmappedSequence=40;
-    /*
-    Quality scores for a read placed near this entry.  Phred units.
-    */
-    optional bytes placedUnmappedQuality=41;
-
-    /*
-    Read name. In SAM/BAM this is referred to as QNAME. Paired and segmented reads will have the same Read name.
-    */
-    optional string readName=42;
-}
-
-/* A link to another alignment entry. This message type is used to represent relations
-   between alignments, such as the relation between the two read fragments in a paired-end protocol,
-   or the relation between parts of reads that align through an exon exon junction and map in
-   different locations of the genome.
-  */
-message RelatedAlignmentEntry {
-    /* Target index of the location where the other alignment entry is mapped.
-      This field is required (enforced by semantic validation in Goby 2.0+).
-    */
-    optional uint32 target_index = 1;
-
-    /* Position on the reference where the other alignment entry is mapped. *
-       This field is required (enforced by semantic validation in Goby 2.0+).
-    */
-    optional uint32 position = 2;
-
-    /* Index of the fragment for the related alignment entry. This index
-       makes it possible to identify which of the read fragments mapped to the given
-       location is related to the source alignment entry.
-       This field is required (enforced by semantic validation in Goby 2.0+).
-    */
-    optional uint32 fragment_index = 3;
-
-    optional uint32 optimized_index=50;
-}
-
-/*
-   Represents sequence variations between the query and the reference sequences. Many variations can be represented.
-   For instance, an insertion at position 5 in the reference would be represented as from="A", to="" position=5.
-   A mutation T->G at position 6 would be rendered as from="T", to="G" position=6. Padded alignments (see SAM description)
-   can be described by a combination of pair-wise alignments, where the gap character '-' is used to indicate that no
-   base exists in the sequence considered for the alignment position, for instance:
-
-   - Padding example:
-
-    123 (<-positions)
-ref A-C
-    A-T [from="-" to=""  position=2] [from="C" to="T"  position=3]
-    ACT [from=""  to="C" position=2] [from="C" to="T"  position=3]
-    A-T [from="-" to=""  position=2] [from="C" to="T"  position=3]
-
-   - Mutation example:
-    123 (<-positions)
-ref ATT
-    ACT [from="T"  to="C" position=2]
-
-    -- Example of deletion in a read:
-    123 (<-positions)
-ref ATT
-    A-T [from="T"  to="-" position=2]
-
-    -- Example of insertion of two base pairs in a read:
-    12345 (<-positions)
-ref A--TT
-    ACCTT [from=""  to="CC" position=2]
-
-  */
-message SequenceVariation {
-    /* The reference bases. Can include one or more gap characters '-', to indicate that the reference sequence has
-     no base at this alignment position.
-     This field is required (enforced by semantic validation in Goby 2.0+).
-    */
-    optional string from = 2;
-    /* The read bases that differ from the reference sequence.  Can include one or more gap characters '-', to indicate
-     that the query sequence has no base at this alignment position.
-     This field is required (enforced by semantic validation in Goby 2.0+).
-    */
-    optional string to = 1;
-    /*
-    The position of the variation on the read, as if the read always matched on the forward strand.
-    Adding position to the index where the reference starts aligning the read yields the position of the variation
-    in reference/target sequence space. Since position starts at one the resulting position will also be one based.
-    This field is required (enforced by semantic validation in Goby 2.0+).
-    */
-    optional uint32 position = 3;
-    /*
-    The position of the variation, starting from the beginning of the aligned read (position 1), and up to the length
-    of the read (inclusive). Use this index if you need to know  how far the variation is observed from the beginning
-    of the sequenced read. When the read has an insertion, this index records the position immediately before the base
-    where the bases are inserted (these bases are in the to field).
-    When the read has a deletion, read_index records the position in the read after which the bases that would align
-    in the reference are missing (these bases are in the from field).
-    This field is required (enforced by semantic validation in Goby 2.0+).
-    */
-    optional uint32 read_index = 5;
-
-    /**
-      The read base quality scores for those bases that are given in the to field. This field
-      is populated when the reads used to perform the search include quality scores, and when
-      the alignment parser can extract the information from the aligner's output.
-      (this option is currently not implemented in Goby.)
-    */
-    optional bytes to_quality = 4;
-
-}
-/*
-  This message is written to 'basename'.header
-*/
-
-message AlignmentHeader {
-    /*
-     The smallest possible query index in this alignment. Data stored as an array where
-     queryIndex is the array index will be stored with only the elements in the inclusive
-     range [smallestSplitQueryIndex largestSplitQueryIndex]
-     Such data structures include queryLength and some arrays in the TooManyHits data
-     structure.
-    */
-    optional uint32 smallest_split_query_index = 9;
-    /*
-     The largest possible query index in this alignment. Data stored as an array where
-     queryIndex is the array index will be stored with only the elements in the inclusive
-     range [smallestSplitQueryIndex largestSplitQueryIndex]
-     Such data structures include queryLength and some arrays in the TooManyHits data
-     structure.
-    */
-    optional uint32 largest_split_query_index = 11;
-
-    /* Mapping from query identifier name to query index (as used in alignment entries).
-    */
-    optional IdentifierMapping query_name_mapping = 1;
-
-    /* Mapping from target identifier name to target index (as used in alignment entries).
-    */
-    optional IdentifierMapping target_name_mapping = 2;
-
-    /*
-     The number of query sequences
-    */
-    optional uint32 number_of_queries = 5;
-    /*
-      The number of target sequences
-    */
-    optional uint32 number_of_targets = 6;
-    /*
-      The number of reads that were aligned to the reference and are represented in this alignment archive.
-    */
-    optional uint32 number_of_aligned_reads = 7;
-
-    /*
-      Length of the query sequences. One number per query, in the order of increasing query index.
-      This information has been moved to the individual alignment entries.
-    */
-    repeated uint32 query_length = 3 [deprecated = true];
-    /*
-       If query length is constant across all the queries, this field contains the constant length.
-       In such cases, query_length will be empty.
-    */
-    optional uint32 constant_query_length = 10;
-
-    /*
-      Length of the target sequences. One number per target, in the order of increasing target index.
-      The target indexes must be 0..(number of targets - 1).
-    */
-    repeated uint32 target_length = 8;
-    /*
-       Indicates whether this alignment is sorted by position. True: the alignment entries occur in sorted
-       order, such that entry a occurs before entry b if a.targetIndex< b.targetIndex or, when entries
-       have the same target, when a.position < b.position.
-    */
-    optional bool sorted = 13;
-
-    /*
-       Indicates whether this alignment is indexed by position. When this attribute is true, a file called
-      'basename'.index exists that contains the AlignmentIndex message (GZip compressed).
-    */
-    optional bool indexed = 14;
-    /*
-      True when query lengths are stored in alignment entries (Goby 1.7+).
-    */
-    optional bool query_lengths_stored_in_entries = 15;
-    /*
-      Name of the aligner that produced this alignment.
-    */
-    optional string aligner_name = 17;
-    /*
-      Version number for the aligner implementation that produced this alignment.
-    */
-    optional string aligner_version = 18;
-    /*
-       The version of Goby that created this alignment file.
-    */
-    optional string version = 25;
-
-    /*
-      Sample basenames, in the order of increasing sampleIndex, starting with sampleIndex=0.
-    */
-
-    repeated string sample_basename = 30;
-
-    /*
-       This field is true when the query indices of alignment entries were permuted to smaller indices. Only sorted
-       alignments can have query_indices_were_permuted=true. When the field is true, and you need to retrieve the
-       original query-index of an alignment (because you want to retrieve the specific read(s) from a read file for
-       instance), you will need the information in the permutation file (extension basename.perm) and transform back
-       each small index of interest to the original query index.
-    */
-    optional bool query_indices_were_permuted = 26;
-    /*
-       This field is true when entries in the alignment .entries file all have the query_index_occurrences field populated
-       (Since Goby 2.0).
-    */
-    optional bool query_index_occurrences = 35;
-
-    /*
-       This field is true when entries in the alignment .entries file all have the ambiguity field populated
-       (Since Goby 2.0).
-    */
-    optional bool ambiguity_stored_in_entries = 36;
-    /*
-       This field is true when entries in the alignment .entries file all have the read_quality_score field populated.
-       (Since Goby 2.0).
-    */
-    optional bool all_read_quality_scores = 40;
-    /*
-      A description of the origin of sets of reads. Serves a similar function to BAM read groups, but more flexible and
-      efficient. Instead of storing strings, we use integers in the entries.
-      Alignemnt entries will link to a specific ReadOriginInfo with the origin_index field.
-      (Since Goby 2.0).
-    */
-    repeated ReadOriginInfo read_origin = 27;
-}
-
-message IdentifierMapping {
-    repeated IdentifierInfo mappings = 1;
-}
-
-message IdentifierInfo {
-    required string name = 1;
-    required uint32 index = 2;
-}
-
-
-/*
-     A description of the origin of sets of reads. Stored in the Goby alignment header and linked
-     from alignment entries. Goby makes it possible to adapt origin equivalence rules on the fly
-     efficiently. To do this, it is sufficient to read the header of the alignment, decide which
-     ReadOriginInfo instances are equivalent (e.g., by looking at sample, platform, library, or
-     other fields in the message), then construct a function e(a):int. This function takes
-     one originIndex parameter and returns another integer that maps to an equivalent class. The
-     equivalence class can be used to estimate error models for entries that belong to each class,
-     for instance.
-     (Since Goby 2.0).
- */
-message ReadOriginInfo {
-    /*
-       Origin index. An integer that links alignment entries to their origin information.
-    */
-    required uint32 origin_index = 1;
-    /*
-       Identifier that describes the origin of the reads. This field is compatible with the ID/platform field of BAM read
-       groups. Free text.
-    */
-    required string origin_id = 2;
-    /*
-       The sample from which the reads were sequenced. This field is compatible with the SM/sample field of BAM read
-       groups. Free text.
-    */
-    optional string sample = 4;
-    /*
-       The platform on which the reads were sequenced. This field is compatible with the PL/platform field of BAM read
-       groups. Valid values: ILLUMINA, SOLID, LS454, HELICOS and PACBIO.
-    */
-    optional string platform = 5;
-    /*
-       The library from which the reads were sequenced. This field is compatible with the LB/library field of BAM read
-       groups. Free text.
-    */
-    optional string library = 8;
-    /*
-       The platform unit on which the reads were sequenced. This field for compatibility with samtools.
-    */
-    optional string platform_unit = 12;
-    /*
-       The date the reads were sequenced. Useful to identify batch effects, in the format dd:MMM:yyyy.
-       The month is Jan, Feb, etc. to avoid all confusion with days when day<=12.
-    */
-    optional string run_date = 6;
-}
-
-/*
-  This message is written to 'basename'.tmh
-*/
-
-message AlignmentTooManyHits {
-    /*
-    The threshold used by the aligner to determine that a query is ambiguous and should be dropped.
-    Referred to as parameter k below.
-    */
-    required uint32 aligner_threshold = 2;
-    /*
-     The hits that are assigned to several (>k) reference location.
-    */
-    repeated AmbiguousLocation hits = 1;
-
-}
-
-message AmbiguousLocation {
-    /*
-     The index of the query that matched too many times.
-    */
-    required uint32 query_index = 1;
-    /*
-     The number of hits that triggered membership in the too many hits list. The query may hit more
-     locations than reported here, since some alignment tools will just drop queries that match above
-     a threshold and stop counting. This number can be >=k.
-    */
-    required uint32 at_least_number_of_hits = 2;
-    /**
-The length of the part of the query sequence that could be matched to the target (also called depth).
-May be less than the length of the query sequence, in which case the match was not perfect. When merging
-alignments produced by searching different reference sequences, consider only at_least_number_of_hits
-from alignments that have exactly the longer depth for the query. */
-    optional uint32 length_of_match = 3;
-}
-
-/*
-      This message is written to 'basename'.index
-  */
-message AlignmentIndex {
-    /*
-      Stores one element by target sequence. Each element is the cumulative target length for the target
-      stored at index i. Assume there are four target sequences, with lengths {10, 12, 15, 34}. The field
-      targetPositionOffsets will contain: {0,10,22,37}. Such offsets can be used to calculate the absolute
-      position of a genomic location. Given targetIndex and positionOnReference, the absolute location
-      is defined as  targetPositionOffsets[targetIndex]+positionOnReference.
-    */
-    repeated uint32 target_position_offsets = 1 [packed = true];
-    /*
-     The byte offsets into the compressed entries file. Byte offsets are matched with absolute position
-     by index. There should be as many elements in offsets as there are in absolutePosition
-     where chunks start which represent entries whose absolute positions are less than
-    */
-    repeated uint64 offsets = 2 [packed = true];
-    /*
-      The absolute positions of the first entry in the chunk that immediately start at offset. One element
-      per chunk in the 'basename'.entries file.
-    */
-    repeated uint64 absolute_positions = 3 [packed = true];
-
-}
diff --git a/sci-biology/goby-cpp/files/Reads.proto b/sci-biology/goby-cpp/files/Reads.proto
deleted file mode 100644
index 32c1244a3eb3..000000000000
--- a/sci-biology/goby-cpp/files/Reads.proto
+++ /dev/null
@@ -1,96 +0,0 @@
-package goby;
-
-option java_package = "edu.cornell.med.icb.goby.reads";
-option optimize_for = SPEED;
-
-message ReadCollection {
-     repeated ReadEntry reads = 1;
-}
-
-message ReadEntry {
-  /*
-    Index of a read.
-  */
-  required uint32 read_index = 1;
-   /*
-    Index of the barcode, if any.
-  */
-  optional uint32 barcode_index = 10;
-  /*
-     Read identifier/name may be present.
-  */
-  optional string read_identifier = 23;
-  /*
-     Additional description about the read (from Fasta/Q format).
-   */
-  optional string description = 22;
-  /*
-    Length of the sequence.
-   */
-  required uint32 read_length = 2;
-  /*
-    Sequence, encoded as ascii characters stored in single bytes.
-   */
-  optional bytes sequence = 3;
-  /*
-   The second sequence in a pair. Stored the same way as the sequence attribute.
-  */
-  optional bytes sequence_pair = 5;
-  /*
-    Length of the second sequence in a pair.
-  */
-  optional uint32 read_length_pair = 6;
-  /*
-    Quality scores in Phred units, stored as single bytes (0-255).
-  */
-  optional bytes quality_scores = 4;
-  /*
-    Quality scores for the second sequence in a pair. Stored as the 'qualityScores' attribute.
-   */
-  optional bytes quality_scores_pair = 7;
-  /*
-    Compressed stream of data. The first byte indicates the compression/decompression method (codec). The remaining bytes are
-    content compressed with the codec.
-  */
-  optional bytes compressed_data = 8;
-  /*
-     Stores meta-data about the reads. Typically meta-data is stored in the very first read of a
-     read collection, with the understanding that the meta-data applies to all the reads in the
-     collection. Meta-data can be used to store information about when the sample was sequenced,
-     or other information of interest. The key-value pair format is sufficiently flexible to
-     accomodate a variety of needs. The following keys are pre-defined. Please use pre-defined
-     keys so that automated tools can use metadata in relatively standard way. Please note that
-     some keys provide a format for the value. This format should also be followed to garantee
-     that meta data can be used computationally in fully automatic manner.
-
-     key="sequencing-run-start-date" value="MM/DD/YYYY" Used to record when the sequencing run
-     was initiated on the instrument. Can be used to detect batch effect in a large set of samples.
-     key="platform" value="<free-text>". Value is free text, but the following terms are pre-defined.
-      Illumina GaIIx
-      Illumina HiSeq 1000
-      Illumina HiSeq 2000
-      Helicos Heliscope
-      LifeTech 5500 SOLiD
-      LifeTech 5500xl SOLiD
-      Roche 454 GS FLX Ti
-
-      key="organism" value="species name"
-      Since Goby 1.9.1
-  */
-  repeated MetaData meta_data = 25;
-
-}
-/*
- A message to store a key/value pair and represent metadata about reads.
- Since Goby 1.9.1
- */
-message MetaData {
- /*
-   Provides the key. See examples in the documentation of meta_data for ReadEntry.
- */
- required string key=1;
- /*
-   Describes the value associated with the key. See examples in the documentation of meta_data for ReadEntry.
- */
- required string value=2;
-}
diff --git a/sci-biology/goby-cpp/files/goby-cpp-2.0.1-underlinking.patch b/sci-biology/goby-cpp/files/goby-cpp-2.0.1-underlinking.patch
deleted file mode 100644
index 415785466af7..000000000000
--- a/sci-biology/goby-cpp/files/goby-cpp-2.0.1-underlinking.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- src/Makefile.am | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/src/Makefile.am b/src/Makefile.am
-index 1033382..33ca906 100644
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -84,7 +84,7 @@ GobyReadsStats_LDADD = libgoby.la ${BOOST_LDFLAGS} ${BOOST_SYSTEM_LIB} ${BOOST_D
- GobyReadsStats_SOURCES = \
- 	GobyReadsStats.cc
- 
--GobyFastaToCompact_LDADD = libgoby.la ${BOOST_LDFLAGS} ${BOOST_SYSTEM_LIB} ${BOOST_DATE_TIME_LIB} ${BOOST_FILESYSTEM_LIB} ${BOOST_PROGRAM_OPTIONS_LIB}
-+GobyFastaToCompact_LDADD = libgoby.la ${BOOST_LDFLAGS} ${BOOST_SYSTEM_LIB} ${BOOST_DATE_TIME_LIB} ${BOOST_FILESYSTEM_LIB} ${BOOST_PROGRAM_OPTIONS_LIB} -lz
- GobyFastaToCompact_SOURCES = \
- 	GobyFastaToCompact.cc
- 
diff --git a/sci-biology/goby-cpp/goby-cpp-2.0.1.ebuild b/sci-biology/goby-cpp/goby-cpp-2.0.1.ebuild
index fcf8971fceb0..e74dd6ecede3 100644
--- a/sci-biology/goby-cpp/goby-cpp-2.0.1.ebuild
+++ b/sci-biology/goby-cpp/goby-cpp-2.0.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -9,7 +9,8 @@ inherit autotools-utils
 
 DESCRIPTION="A DNA sequencing data management framework - C/C++ API"
 HOMEPAGE="http://campagnelab.org/software/goby/"
-SRC_URI="http://chagall.med.cornell.edu/goby/releases/archive/release-goby_${PV}/goby_${PV}-cpp.zip"
+SRC_URI="http://chagall.med.cornell.edu/goby/releases/archive/release-goby_${PV}/goby_${PV}-cpp.zip
+	https://dev.gentoo.org/~mgorny/dist/${P}-files.tar.bz2"
 
 LICENSE="GPL-3"
 SLOT="0"
@@ -24,7 +25,7 @@ RDEPEND="${DEPEND}"
 S="${WORKDIR}/${PV}/cpp"
 
 PATCHES=(
-	"${FILESDIR}"/${P}-underlinking.patch
+	"${WORKDIR}"/${P}-files/${P}-underlinking.patch
 )
 
 src_prepare() {
@@ -33,7 +34,7 @@ src_prepare() {
 		-i src/Makefile.am || die
 
 	pushd src/goby > /dev/null || die
-	cp "${FILESDIR}"/*.proto . || die
+	cp "${WORKDIR}"/${P}-files/*.proto . || die
 	protoc --cpp_out=. *.proto || die
 	popd > /dev/null || die
 
diff --git a/sci-biology/rmblast/Manifest b/sci-biology/rmblast/Manifest
index 46de8283053e..10b761c8a307 100644
--- a/sci-biology/rmblast/Manifest
+++ b/sci-biology/rmblast/Manifest
@@ -1,4 +1,4 @@
-AUX rmblast-1.2-gcc47.patch 31795 BLAKE2B 65a82f097c25d9619c93c8b6f0b95bbb73cd981843201342cc34ce2eb6909844cd2a3463e324f11b61a7e4a855343787c9c320fdfdbdf78f1d3e55ce3e2b89b3 SHA512 2db82b02b157dd39c21d1fc459c4837741088d0d764c994094096c15ce76331f33f68e7e8498f7ea43e4979cde2fd248baf0687ac08b147d1060b54ac55b83d0
-DIST rmblast-1.2-ncbi-blast-2.2.23+-src.tar.gz 10744076 SHA256 996be9886189364fff8ed39d4668122b2e5b8b010be47d929602416d95628eef SHA512 e7c2ebd114aee045ea3f3f462cf2658440e13a2d1eb777648386e1c5eeda9f8083af383c019f9b5802d935d6eb2367eef20822afc45233ddb44a426b4dd7ddb6 WHIRLPOOL aa3ada4297812a97614b0fe218de65d7474edfb5910e156eb09b625d45338a97b35f46876f5edf6105ead8b321a28f55ed7de2ad251bbc48ffd0cfa65ee2ac7a
-EBUILD rmblast-1.2-r1.ebuild 1137 BLAKE2B 201c0a80c735587a4ce53d7af48292bddbb1400d3f710224ebc111bc626220b42e2435207725076183d313c2c385627e176de0d056a5c446e3dbd2a4d16773ad SHA512 9b624dd651e7f8988e4ae605a737c2baaa55681e30af93627b3824004d487bc94d6a389368e465c1fa74d2783342b10a41ac8c8aabee3691099e115f62c682f6
+DIST rmblast-1.2-gcc47.patch.bz2 7803 BLAKE2B cd3bb1aa2b6eb9e188f28589d42ce91f027866d91013f2a6123ee61e7ce28f980b858e775bc15313cf1573f0bc827f9e663d46c1bd0d2fe218745cfbbc3781a1 SHA512 4cd72dd5c777ad866b9cf674384872de5424404b524ac536e58ab412b98b6601aa5f609d05ea2329b77f16e7aca215bbc6eb3531652e5fe81e48cf997b56d13b
+DIST rmblast-1.2-ncbi-blast-2.2.23+-src.tar.gz 10744076 BLAKE2B 6539ec8fcd345bcc1c3ecede6acec233cdc343c3df18748e195dc525f4a65fefeee8398471a26dc671bfed8612e010c26b7a8a66a3c7198f142c2e068ff72751 SHA512 e7c2ebd114aee045ea3f3f462cf2658440e13a2d1eb777648386e1c5eeda9f8083af383c019f9b5802d935d6eb2367eef20822afc45233ddb44a426b4dd7ddb6
+EBUILD rmblast-1.2-r1.ebuild 1194 BLAKE2B a9a30ea494d819720a50c194d80d8f63141c9f37101dbb8b2bbbaf79938aa2a21910932a1339bc944d4270c050633fa5a81ced90ddf43800710aa38211f5880d SHA512 75821816764975bbc935ff0e2edf4b0b30e9f8b5cad2e236512993da1cada6079876a36c7ee87aa9c1e95c7ce38e720ade531f0e261559571398d80364be0d2a
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/rmblast/files/rmblast-1.2-gcc47.patch b/sci-biology/rmblast/files/rmblast-1.2-gcc47.patch
deleted file mode 100644
index 70200d59ea4a..000000000000
--- a/sci-biology/rmblast/files/rmblast-1.2-gcc47.patch
+++ /dev/null
@@ -1,865 +0,0 @@
- c++/include/corelib/ncbiexpt.hpp                   |   4 +-
- c++/include/corelib/ncbimisc.hpp                   |   2 +
- c++/include/corelib/ncbiobj.hpp                    |   2 +-
- c++/include/corelib/ncbistl.hpp                    |   6 +-
- c++/include/corelib/ncbistr.hpp                    |   2 +-
- c++/include/corelib/test_boost.hpp                 |  44 +++++-
- c++/include/dbapi/driver/dbapi_object_convert.hpp  |   8 +-
- .../dbapi/driver/impl/dbapi_driver_utils.hpp       |   2 +-
- c++/include/serial/impl/stltypes.hpp               |  16 ++-
- c++/include/serial/iterator.hpp                    |   6 +-
- c++/include/serial/serialbase.hpp                  |   8 +-
- c++/include/util/bitset/bmfunc.h                   |   7 +
- c++/include/util/linkedset.hpp                     |  16 +--
- c++/include/util/rangemap.hpp                      |   4 +-
- c++/src/connect/ncbi_gnutls.c                      |  19 ++-
- c++/src/corelib/ncbifile.cpp                       |   2 +-
- c++/src/corelib/test_boost.cpp                     | 156 ++++++++++++++++++++-
- c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp  |   2 +-
- c++/src/serial/stdtypes.cpp                        |   8 +-
- 19 files changed, 269 insertions(+), 45 deletions(-)
-
-diff --git a/c++/include/corelib/ncbiexpt.hpp b/c++/include/corelib/ncbiexpt.hpp
-index a9cf850..6d90e74 100644
---- a/c++/include/corelib/ncbiexpt.hpp
-+++ b/c++/include/corelib/ncbiexpt.hpp
-@@ -831,7 +831,7 @@ const TTo* UppermostCast(const TFrom& from)
-     exception_class(const exception_class& other) \
-        : base_class(other) \
-     { \
--        x_Assign(other); \
-+        this->x_Assign(other); \
-     } \
- public: \
-     virtual ~exception_class(void) throw() {} \
-@@ -1154,7 +1154,7 @@ public:
-         : TBase( other)
-     {
-         m_Errno = other.m_Errno;
--        x_Assign(other);
-+        this->x_Assign(other);
-     }
- 
-     /// Destructor.
-diff --git a/c++/include/corelib/ncbimisc.hpp b/c++/include/corelib/ncbimisc.hpp
-index f45d280..f0c030d 100644
---- a/c++/include/corelib/ncbimisc.hpp
-+++ b/c++/include/corelib/ncbimisc.hpp
-@@ -57,6 +57,8 @@
-  * @{
-  */
- 
-+#include <stdlib.h>
-+
- #ifndef NCBI_ESWITCH_DEFINED
- #define NCBI_ESWITCH_DEFINED
- 
-diff --git a/c++/include/corelib/ncbiobj.hpp b/c++/include/corelib/ncbiobj.hpp
-index 4f83db4..815c188 100644
---- a/c++/include/corelib/ncbiobj.hpp
-+++ b/c++/include/corelib/ncbiobj.hpp
-@@ -2128,7 +2128,7 @@ public:
-         CIRef<Interface, TThisType> ref(
-                    dynamic_cast<Interface*>(proxy->GetLockedObject()), *this);
-         if (ref.NotNull()) {
--            Unlock(ref.GetPointer());
-+            this->Unlock(ref.GetPointer());
-         }
-         return ref;
-     }
-diff --git a/c++/include/corelib/ncbistl.hpp b/c++/include/corelib/ncbistl.hpp
-index 0bf465a..0618d9d 100644
---- a/c++/include/corelib/ncbistl.hpp
-+++ b/c++/include/corelib/ncbistl.hpp
-@@ -37,7 +37,6 @@
- 
- #include <common/ncbi_export.h>
- 
--
- // Get rid of some warnings in MSVC++ 6.00
- #if (_MSC_VER >= 1200)
- // too long identificator name in the debug info;  truncated
-@@ -162,6 +161,9 @@ typedef int NCBI_NAME2(T_EAT_SEMICOLON_,UniqueName)
- #endif
- 
- #if defined(NCBI_COMPILER_GCC) || defined(NCBI_COMPILER_WORKSHOP)
-+#  if defined(NCBI_COMPILER_GCC)  &&  NCBI_COMPILER_VERSION >= 400
-+#    include <algorithm>
-+#  endif
- // This template is used by some stl algorithms (sort, reverse...)
- // We need to have our own implementation because some C++ Compiler vendors 
- // implemented it by using a temporary variable and an assignment operator 
-@@ -174,7 +176,7 @@ template<typename Iter>
- inline
- void iter_swap( Iter it1, Iter it2 )
- {
--    swap( *it1, * it2 );
-+    swap( *it1, *it2 );
- }
- 
- END_STD_SCOPE
-diff --git a/c++/include/corelib/ncbistr.hpp b/c++/include/corelib/ncbistr.hpp
-index db7054f..63e3299 100644
---- a/c++/include/corelib/ncbistr.hpp
-+++ b/c++/include/corelib/ncbistr.hpp
-@@ -2583,7 +2583,7 @@ public:
-         : TBase(other)
-     {
-         m_Pos = other.m_Pos;
--        x_Assign(other);
-+        this->x_Assign(other);
-     }
- 
-     /// Destructor.
-diff --git a/c++/include/corelib/test_boost.hpp b/c++/include/corelib/test_boost.hpp
-index 69c41f3..4cd77d3 100644
---- a/c++/include/corelib/test_boost.hpp
-+++ b/c++/include/corelib/test_boost.hpp
-@@ -56,10 +56,18 @@
- #  undef BOOST_AUTO_TEST_MAIN
- #endif
- 
-+#ifdef NCBI_COMPILER_MSVC
-+#  pragma warning(push)
-+// 'class' : class has virtual functions, but destructor is not virtual
-+#  pragma warning(disable: 4265)
-+#endif
-+
-+#include <boost/version.hpp>
- #include <boost/test/auto_unit_test.hpp>
- #include <boost/test/floating_point_comparison.hpp>
- #include <boost/test/framework.hpp>
- #include <boost/test/execution_monitor.hpp>
-+#include <boost/test/parameterized_test.hpp>
- 
- #include <boost/preprocessor/tuple/rem.hpp>
- #include <boost/preprocessor/repeat.hpp>
-@@ -72,6 +80,7 @@
- #undef BOOST_CHECK_THROW_IMPL
- #undef BOOST_CHECK_NO_THROW_IMPL
- #undef BOOST_FIXTURE_TEST_CASE
-+#undef BOOST_PARAM_TEST_CASE
- 
- #define BOOST_CHECK_THROW_IMPL( S, E, P, prefix, TL )                    \
- try {                                                                    \
-@@ -109,6 +118,12 @@ catch( ... ) {                                                               \
- }                                                                            \
- /**/
- 
-+#if BOOST_VERSION >= 104200
-+#  define NCBI_BOOST_LOCATION()  , boost::execution_exception::location()
-+#else
-+#  define NCBI_BOOST_LOCATION()
-+#endif
-+
- #define BOOST_FIXTURE_TEST_CASE( test_name, F )                         \
- struct test_name : public F { void test_method(); };                    \
-                                                                         \
-@@ -124,7 +139,8 @@ static void BOOST_AUTO_TC_INVOKER( test_name )()                        \
-                          ::framework::current_test_case().p_name        \
-                  << "\"" << ex);                                        \
-         throw boost::execution_exception(                               \
--                boost::execution_exception::cpp_exception_error, "");   \
-+                boost::execution_exception::cpp_exception_error, ""     \
-+                NCBI_BOOST_LOCATION() );                                \
-     }                                                                   \
- }                                                                       \
-                                                                         \
-@@ -142,6 +158,12 @@ BOOST_JOIN( BOOST_JOIN( test_name, _registrar ), __LINE__ ) (           \
- void test_name::test_method()                                           \
- /**/
- 
-+#define BOOST_PARAM_TEST_CASE( function, begin, end )                       \
-+    ::NCBI_NS_NCBI::NcbiTestGenTestCases( function,                         \
-+                                          BOOST_TEST_STRINGIZE( function ), \
-+                                          (begin), (end) )                  \
-+/**/
-+
- /// Set timeout value for the test case created using auto-registration
- /// facility.
- #define BOOST_AUTO_TEST_CASE_TIMEOUT(test_name, n)                      \
-@@ -158,6 +180,26 @@ static struct BOOST_JOIN( test_name, _timeout_spec )                    \
- } BOOST_JOIN( test_name, _timeout_spec_inst );                          \
- /**/
- 
-+/// Automatic registration of the set of test cases based on some function
-+/// accepting one parameter. Set of parameters used to call that function is
-+/// taken from iterator 'begin' which is incremented until it reaches 'end'.
-+///
-+/// @sa BOOST_PARAM_TEST_CASE
-+#define BOOST_AUTO_PARAM_TEST_CASE( function, begin, end )               \
-+    BOOST_AUTO_TU_REGISTRAR(function) (                                  \
-+                            BOOST_PARAM_TEST_CASE(function, begin, end)) \
-+/**/
-+
-+#define BOOST_TIMEOUT(M)                                        \
-+    do {                                                        \
-+        static string s(M);                                     \
-+        throw boost::execution_exception(                       \
-+                boost::execution_exception::timeout_error, s    \
-+                NCBI_BOOST_LOCATION());                         \
-+    } while (0)                                                 \
-+/**/
-+
-+
- 
- #define NCBITEST_CHECK_IMPL(P, check_descr, TL, CT)                          \
-     BOOST_CHECK_NO_THROW_IMPL(BOOST_CHECK_IMPL(P, check_descr, TL, CT), TL)
-diff --git a/c++/include/dbapi/driver/dbapi_object_convert.hpp b/c++/include/dbapi/driver/dbapi_object_convert.hpp
-index 6fcde61..eddde81 100644
---- a/c++/include/dbapi/driver/dbapi_object_convert.hpp
-+++ b/c++/include/dbapi/driver/dbapi_object_convert.hpp
-@@ -67,7 +67,7 @@ public:
-     operator const CTime&(void) const;
- 
- private:
--    mutable obj_type& m_Value; 
-+    obj_type& m_Value; 
- };
- 
- ////////////////////////////////////////////////////////////////////////////////
-@@ -92,7 +92,7 @@ public:
-     operator const CTime&(void) const;
- 
- private:
--    mutable obj_type& m_Value; 
-+    obj_type& m_Value; 
- };
- 
- ////////////////////////////////////////////////////////////////////////////////
-@@ -133,7 +133,7 @@ public:
-     operator const CTime&(void) const;
- 
- private:
--    mutable obj_type& m_Value; 
-+    obj_type& m_Value; 
- };
- 
- ////////////////////////////////////////////////////////////////////////////////
-@@ -174,7 +174,7 @@ public:
-     operator const CTime&(void) const;
- 
- private:
--    mutable obj_type& m_Value; 
-+    obj_type& m_Value; 
- };
- 
- ////////////////////////////////////////////////////////////////////////////////
-diff --git a/c++/include/dbapi/driver/impl/dbapi_driver_utils.hpp b/c++/include/dbapi/driver/impl/dbapi_driver_utils.hpp
-index 0792a6d..b6bd64b 100644
---- a/c++/include/dbapi/driver/impl/dbapi_driver_utils.hpp
-+++ b/c++/include/dbapi/driver/impl/dbapi_driver_utils.hpp
-@@ -231,7 +231,7 @@ protected:
- 
- private:
-     const string& m_SPName;
--    mutable impl::CConnection& m_Conn;
-+    impl::CConnection& m_Conn;
- };
- 
- 
-diff --git a/c++/include/serial/impl/stltypes.hpp b/c++/include/serial/impl/stltypes.hpp
-index d41ab94..7d9e3ce 100644
---- a/c++/include/serial/impl/stltypes.hpp
-+++ b/c++/include/serial/impl/stltypes.hpp
-@@ -412,6 +412,7 @@ public:
-     typedef StlIterator TStlIterator;
-     typedef TypeInfoIterator TTypeInfoIterator;
-     typedef typename TTypeInfoIterator::TObjectPtr TObjectPtr;
-+    typedef CStlClassInfoFunctions<Container> CParent;
- 
-     static TStlIterator& It(TTypeInfoIterator& iter)
-         {
-@@ -437,7 +438,8 @@ public:
-         }
-     static bool InitIterator(TTypeInfoIterator& iter)
-         {
--            TStlIterator stl_iter = Get(iter.GetContainerPtr()).begin();
-+            TStlIterator stl_iter
-+                = CParent::Get(iter.GetContainerPtr()).begin();
-             if ( sizeof(TStlIterator) <= sizeof(iter.m_IteratorData) ) {
-                 void* data = &iter.m_IteratorData;
-                 new (data) TStlIterator(stl_iter);
-@@ -445,7 +447,7 @@ public:
-             else {
-                 iter.m_IteratorData = new TStlIterator(stl_iter);
-             }
--            return stl_iter != Get(iter.GetContainerPtr()).end();
-+            return stl_iter != CParent::Get(iter.GetContainerPtr()).end();
-         }
-     static void ReleaseIterator(TTypeInfoIterator& iter)
-         {
-@@ -466,7 +468,7 @@ public:
- 
-     static bool NextElement(TTypeInfoIterator& iter)
-         {
--            return ++It(iter) != Get(iter.GetContainerPtr()).end();
-+            return ++It(iter) != CParent::Get(iter.GetContainerPtr()).end();
-         }
-     static TObjectPtr GetElementPtr(const TTypeInfoIterator& iter)
-         {
-@@ -503,7 +505,7 @@ public:
-     
-     static bool EraseElement(TTypeInfoIterator& iter)
-         {
--            TStlIterator& it = It(iter);
-+            TStlIterator& it = CParent::It(iter);
-             Container* c = static_cast<Container*>(iter.GetContainerPtr());
-             it = c->erase(it);
-             return it != c->end();
-@@ -511,7 +513,7 @@ public:
-     static void EraseAllElements(TTypeInfoIterator& iter)
-         {
-             Container* c = static_cast<Container*>(iter.GetContainerPtr());
--            c->erase(It(iter), c->end());
-+            c->erase(CParent::It(iter), c->end());
-         }
- 
-     static void SetIteratorFunctions(CStlOneArgTemplate* info)
-@@ -542,7 +544,7 @@ public:
-         }
-     static bool EraseElement(TTypeInfoIterator& iter)
-         {
--            TStlIterator& it = It(iter);
-+            TStlIterator& it = CParent::It(iter);
-             Container* c = static_cast<Container*>(iter.GetContainerPtr());
-             TStlIterator erase = it++;
-             c->erase(erase);
-@@ -551,7 +553,7 @@ public:
-     static void EraseAllElements(TTypeInfoIterator& iter)
-         {
-             Container* c = static_cast<Container*>(iter.GetContainerPtr());
--            c->erase(It(iter), c->end());
-+            c->erase(CParent::It(iter), c->end());
-         }
- 
-     static void SetIteratorFunctions(CStlOneArgTemplate* info)
-diff --git a/c++/include/serial/iterator.hpp b/c++/include/serial/iterator.hpp
-index 25e1193..cddb046 100644
---- a/c++/include/serial/iterator.hpp
-+++ b/c++/include/serial/iterator.hpp
-@@ -491,13 +491,13 @@ protected:
-     CTypeIteratorBase(TTypeInfo needType, const TBeginInfo& beginInfo)
-         : m_NeedType(needType)
-         {
--            Init(beginInfo);
-+            this->Init(beginInfo);
-         }
-     CTypeIteratorBase(TTypeInfo needType, const TBeginInfo& beginInfo,
-                       const string& filter)
-         : m_NeedType(needType)
-         {
--            Init(beginInfo, filter);
-+            this->Init(beginInfo, filter);
-         }
- 
-     virtual bool CanSelect(const CConstObjectInfo& object)
-@@ -599,7 +599,7 @@ public:
- 
-     CTypesIteratorBase<Parent>& operator=(const TBeginInfo& beginInfo)
-         {
--            Init(beginInfo);
-+            this->Init(beginInfo);
-             return *this;
-         }
- 
-diff --git a/c++/include/serial/serialbase.hpp b/c++/include/serial/serialbase.hpp
-index be6a4f9..d59fb25 100644
---- a/c++/include/serial/serialbase.hpp
-+++ b/c++/include/serial/serialbase.hpp
-@@ -364,11 +364,15 @@ public:
-     // cast to object type
-     TObject& operator*(void)
-         {
--            return *reinterpret_cast<TObject*>(m_Buffer);
-+            TObject* ptr = static_cast<TObject*>
-+                (static_cast<void*>(m_Buffer));
-+            return *ptr;
-         }
-     const TObject& operator*(void) const
-         {
--            return *reinterpret_cast<const TObject*>(m_Buffer);
-+            const TObject* ptr = static_cast<const TObject*>
-+                (static_cast<const void*>(m_Buffer));
-+            return *ptr;
-         }
- 
-     // construct/destruct object
-diff --git a/c++/include/util/bitset/bmfunc.h b/c++/include/util/bitset/bmfunc.h
-index 5917ee5..a8c204b 100644
---- a/c++/include/util/bitset/bmfunc.h
-+++ b/c++/include/util/bitset/bmfunc.h
-@@ -37,6 +37,13 @@ For more information please visit:  http://bmagic.sourceforge.net
- namespace bm
- {
- 
-+bm::id_t bit_block_any_range(const bm::word_t* block,
-+                             bm::word_t left,
-+                             bm::word_t right);
-+
-+bm::id_t bit_block_calc_count_range(const bm::word_t* block,
-+                                    bm::word_t left,
-+                                    bm::word_t right);
- 
- /*!
-     @brief Structure with statistical information about bitset's memory 
-diff --git a/c++/include/util/linkedset.hpp b/c++/include/util/linkedset.hpp
-index e8bbe6e..364164b 100644
---- a/c++/include/util/linkedset.hpp
-+++ b/c++/include/util/linkedset.hpp
-@@ -268,10 +268,10 @@ public:
-             pair<iterator, bool> ins = m_Container.insert(value);
-             if ( ins.second ) {
-                 if ( ins.first == begin() )
--                    insertToStart(*ins.first);
-+                    this->insertToStart(*ins.first);
-                 else {
-                     iterator prev = ins.first;
--                    insertAfter(*--prev, *ins.first);
-+                    this->insertAfter(*--prev, *ins.first);
-                 }
-             }
-             return ins;
-@@ -280,10 +280,10 @@ public:
-     void erase(iterator iter)
-         {
-             if ( iter == begin() )
--                removeFromStart(*iter);
-+                this->removeFromStart(*iter);
-             else {
-                 iterator prev = iter;
--                removeAfter(*--prev, *iter);
-+                this->removeAfter(*--prev, *iter);
-             }
-             m_Container.erase(iter);
-         }
-@@ -422,10 +422,10 @@ public:
-         {
-             iterator iter = m_Container.insert(value);
-             if ( iter == begin() )
--                insertToStart(get(iter));
-+                this->insertToStart(get(iter));
-             else {
-                 iterator prev = iter;
--                insertAfter(get(--prev), get(iter));
-+                this->insertAfter(get(--prev), get(iter));
-             }
-             return iter;
-         }
-@@ -433,10 +433,10 @@ public:
-     void erase(iterator iter)
-         {
-             if ( iter == begin() )
--                removeFromStart(get(iter));
-+                this->removeFromStart(get(iter));
-             else {
-                 iterator prev = iter;
--                removeAfter(get(--prev), get(iter));
-+                this->removeAfter(get(--prev), get(iter));
-             }
-             m_Container.erase(iter);
-         }
-diff --git a/c++/include/util/rangemap.hpp b/c++/include/util/rangemap.hpp
-index c4f5f37..56e267d 100644
---- a/c++/include/util/rangemap.hpp
-+++ b/c++/include/util/rangemap.hpp
-@@ -578,7 +578,7 @@ public:
-             // get level
- 
-             // insert element
--            TSelectMapI selectIter = insertLevel(selectKey);
-+            TSelectMapI selectIter = this->insertLevel(selectKey);
-             pair<TLevelMapI, bool> levelIns = selectIter->second.insert(value);
-             
-             pair<iterator, bool> ret;
-@@ -640,7 +640,7 @@ public:
-             // insert element
-             iterator ret;
-             ret.m_Range = range_type::GetWhole();
--            ret.m_SelectIter = insertLevel(selectKey);
-+            ret.m_SelectIter = this->insertLevel(selectKey);
-             ret.m_SelectIterEnd = this->m_SelectMap.end();
-             ret.m_LevelIter = ret.m_SelectIter->second.insert(value);
-             return ret;
-diff --git a/c++/src/connect/ncbi_gnutls.c b/c++/src/connect/ncbi_gnutls.c
-index f0242b7..8b13713 100644
---- a/c++/src/connect/ncbi_gnutls.c
-+++ b/c++/src/connect/ncbi_gnutls.c
-@@ -98,7 +98,6 @@ static const int kGnuTlsCertPrio[] = {
-     0
- };
- static const int kGnuTlsCompPrio[] = {
--    GNUTLS_COMP_LZO,
-     GNUTLS_COMP_ZLIB,
-     GNUTLS_COMP_NULL,
-     0
-@@ -254,6 +253,24 @@ static EIO_Status s_GnuTlsOpen(void* session, int* error)
- }
- 
- 
-+/*ARGSUSED*/
-+static void x_set_errno(gnutls_session_t session, int error)
-+{
-+#  ifdef LIBGNUTLS_VERSION_NUMBER
-+#    if                                         \
-+    LIBGNUTLS_VERSION_MAJOR > 1  ||             \
-+    LIBGNUTLS_VERSION_MINOR > 5  ||             \
-+    LIBGNUTLS_VERSION_PATCH > 3
-+    gnutls_transport_set_errno(session, error);
-+    return;
-+#    endif /*LIBGNUTLS_VERSION >= 1.5.4*/
-+#  endif /*LIBGNUTLS_VERSION_NUMBER*/
-+    /*NOTREACHED*/
-+    if (error)
-+        errno = error;
-+}
-+
-+
- static ssize_t x_GnuTlsPull(gnutls_transport_ptr_t ptr,
-                             void* buf, size_t size)
- {
-diff --git a/c++/src/corelib/ncbifile.cpp b/c++/src/corelib/ncbifile.cpp
-index d751e62..fdc81c7 100644
---- a/c++/src/corelib/ncbifile.cpp
-+++ b/c++/src/corelib/ncbifile.cpp
-@@ -51,8 +51,8 @@
- #  include <dirent.h>
- #  include <pwd.h>
- #  include <fcntl.h>
--#  include <sys/time.h>
- #  include <sys/mman.h>
-+#  include <sys/time.h>
- #  ifdef HAVE_SYS_STATVFS_H
- #    include <sys/statvfs.h>
- #  endif
-diff --git a/c++/src/corelib/test_boost.cpp b/c++/src/corelib/test_boost.cpp
-index dfd9cc8..f93d2ca 100644
---- a/c++/src/corelib/test_boost.cpp
-+++ b/c++/src/corelib/test_boost.cpp
-@@ -41,6 +41,7 @@
- #ifndef BOOST_TEST_NO_LIB
- #  define BOOST_TEST_NO_LIB
- #endif
-+#define BOOST_TEST_NO_MAIN
- #include <corelib/test_boost.hpp>
- 
- #include <boost/preprocessor/cat.hpp>
-@@ -95,6 +96,7 @@ const char* kTestResultTimeout     = "timeout";
- const char* kTestResultAborted     = "aborted";
- const char* kTestResultSkipped     = "skipped";
- const char* kTestResultDisabled    = "disabled";
-+const char* kTestResultToFix       = "tofix";
- 
- 
- typedef but::results_reporter::format   TBoostRepFormatter;
-@@ -168,14 +170,24 @@ public:
-                                           unsigned long elapsed);
-     virtual
-     void test_unit_skipped(ostream& ostr, but::test_unit const& tu);
-+#if BOOST_VERSION >= 104200
-+    virtual
-+    void log_exception    (ostream& ostr, but::log_checkpoint_data const& lcd,
-+                                          boost::execution_exception const& ex);
-+    // Next line is necessary for compiling with ICC and Boost 1.41.0 and up
-+    using TBoostLogFormatter::log_exception;
-+#else
-     virtual
-     void log_exception    (ostream& ostr, but::log_checkpoint_data const& lcd,
-                                           but::const_string explanation);
-+#endif
-     virtual
-     void log_entry_start  (ostream& ostr, but::log_entry_data const& led,
-                                           log_entry_types let);
-     virtual
-     void log_entry_value  (ostream& ostr, but::const_string value);
-+    // Next line is necessary for compiling with ICC and Boost 1.41.0 and up
-+    using TBoostLogFormatter::log_entry_value;
-     virtual
-     void log_entry_finish (ostream& ostr);
- 
-@@ -402,10 +414,15 @@ public:
- 
-     /// Mark test case as failed due to hit of the timeout
-     void SetTestTimedOut(but::test_case* tc);
-+    /// Register the fact of test failure
-+    void SetTestErrored(but::test_case* tc);
-+    /// Check if given test is marked as requiring fixing in the future
-+    bool IsTestToFix(const but::test_unit* tu);
- 
-     /// Get number of actually executed tests
-     int GetRanTestsCount(void);
--
-+    /// Get number of tests that were failed but are marked to be fixed
-+    int GetToFixTestsCount(void);
-     /// Get string representation of result of test execution
-     string GetTestResultString(but::test_unit* tu);
- 
-@@ -415,6 +432,11 @@ public:
-     /// Check if user initialization functions failed
-     bool IsInitFailed(void);
- 
-+    /// Check if there were any test errors
-+    bool HasTestErrors(void);
-+    /// Check if there were any timeouted tests
-+    bool HasTestTimeouts(void);
-+
- private:
-     typedef list<TNcbiTestUserFunction> TUserFuncsList;
- 
-@@ -493,6 +515,8 @@ private:
-     TUnitsSet                 m_DisabledTests;
-     /// List of all tests which result is a timeout
-     TUnitsSet                 m_TimedOutTests;
-+    /// List of all tests marked as in need of fixing in the future
-+    TUnitsSet                 m_ToFixTests;
-     /// List of all dependencies for each test having dependencies
-     TUnitToManyMap            m_TestDeps;
-     /// Observer to make test dependencies and look for unit's timeouts
-@@ -512,12 +536,18 @@ private:
-     /// String representation for whole test timeout (real value taken from
-     /// CHECK_TIMEOUT in Makefile).
-     string                    m_TimeoutStr;
-+    /// Multiplicator for timeouts
-+    double                    m_TimeMult;
-     /// Timer measuring elapsed time for the whole test
-     CStopWatch                m_Timer;
-     /// Timeout that was set in currently executing unit before adjustment
-     ///
-     /// @sa AdjustTestTimeout()
-     unsigned int              m_CurUnitTimeout;
-+    /// Flag showing if there were some test errors
-+    bool                      m_HasTestErrors;
-+    /// Flag showing if there were some timeouted tests
-+    bool                      m_HasTestTimeouts;
- };
- 
- 
-@@ -794,7 +824,10 @@ CNcbiTestApplication::CNcbiTestApplication(void)
-       m_RunMode  (0),
-       m_DummyTest(NULL),
-       m_Timeout  (0),
--      m_Timer    (CStopWatch::eStart)
-+      m_TimeMult (1),
-+      m_Timer    (CStopWatch::eStart),
-+      m_HasTestErrors(false),
-+      m_HasTestTimeouts(false)
- {
-     m_Reporter = new CNcbiBoostReporter();
-     m_Logger   = new CNcbiBoostLogger();
-@@ -1244,6 +1277,24 @@ CNcbiTestApplication::GetRanTestsCount(void)
-     return result;
- }
- 
-+int
-+CNcbiTestApplication::GetToFixTestsCount(void)
-+{
-+    int result = 0;
-+    ITERATE(TUnitsSet, it, m_ToFixTests) {
-+        if (!but::results_collector.results((*it)->p_id).passed())
-+            ++result;
-+    }
-+    return result;
-+}
-+
-+inline bool
-+CNcbiTestApplication::IsTestToFix(const but::test_unit* tu)
-+{
-+    return m_ToFixTests.find(const_cast<but::test_unit*>(tu))
-+                                                        != m_ToFixTests.end();
-+}
-+
- inline void
- CNcbiTestApplication::x_SetupBoostReporters(void)
- {
-@@ -1391,6 +1442,18 @@ CNcbiTestApplication::InitTestFramework(int argc, char* argv[])
-     return NULL;
- }
- 
-+inline bool
-+CNcbiTestApplication::HasTestErrors(void)
-+{
-+    return m_HasTestErrors;
-+}
-+
-+inline bool
-+CNcbiTestApplication::HasTestTimeouts(void)
-+{
-+    return m_HasTestTimeouts;
-+}
-+
- void
- CNcbiTestsCollector::visit(but::test_case const& test)
- {
-@@ -1431,9 +1494,20 @@ CNcbiTestsObserver::test_unit_finish(but::test_unit const& tu,
-     // elapsed comes in microseconds
-     if (timeout != 0  &&  timeout < elapsed / 1000000) {
-         boost::execution_exception ex(
--               boost::execution_exception::timeout_error, "Timeout exceeded");
-+               boost::execution_exception::timeout_error, "Timeout exceeded"
-+               NCBI_BOOST_LOCATION());
-         but::framework::exception_caught(ex);
-     }
-+
-+    but::test_results& tr = but::s_rc_impl().m_results_store[tu.p_id];
-+    if (!tr.passed()  &&  s_GetTestApp().IsTestToFix(&tu)) {
-+        static_cast<but::readwrite_property<bool>& >(
-+            static_cast<but::class_property<bool>& >(
-+                                            tr.p_skipped)).set(true);
-+        static_cast<but::readwrite_property<but::counter_t>& >(
-+            static_cast<but::class_property<but::counter_t>& >(
-+                                            tr.p_assertions_failed)).set(0);
-+    }
- }
- 
- void
-@@ -1551,12 +1625,21 @@ CNcbiBoostLogger::test_unit_skipped(ostream& ostr, but::test_unit const& tu)
-     m_Upper->test_unit_skipped(ostr, tu);
- }
- 
-+#if BOOST_VERSION >= 104200
-+void
-+CNcbiBoostLogger::log_exception(ostream& ostr, but::log_checkpoint_data const& lcd,
-+                                boost::execution_exception const& ex)
-+{
-+    m_Upper->log_exception(ostr, lcd, ex);
-+}
-+#else
- void
- CNcbiBoostLogger::log_exception(ostream& ostr, but::log_checkpoint_data const& lcd,
-                                 but::const_string explanation)
- {
-     m_Upper->log_exception(ostr, lcd, explanation);
- }
-+#endif
- 
- void
- CNcbiBoostLogger::log_entry_start(ostream& ostr, but::log_entry_data const& led,
-@@ -1631,9 +1714,74 @@ NcbiTestGetUnit(CTempString test_name)
- END_NCBI_SCOPE
- 
- 
-+using namespace but;
-+
- /// Global initialization function called from Boost framework
--but::test_suite*
-+test_suite*
- init_unit_test_suite(int argc, char* argv[])
- {
-     return NCBI_NS_NCBI::s_GetTestApp().InitTestFramework(argc, argv);
- }
-+
-+// This main() is mostly a copy from Boost's unit_test_main.ipp
-+int
-+main(int argc, char* argv[])
-+{
-+    int result = boost::exit_success;
-+
-+    try {
-+        framework::init( &init_unit_test_suite, argc, argv );
-+
-+        if( !runtime_config::test_to_run().is_empty() ) {
-+            test_case_filter filter( runtime_config::test_to_run() );
-+
-+            traverse_test_tree( framework::master_test_suite().p_id, filter );
-+        }
-+
-+        framework::run();
-+
-+        // Let's try to make report in case of any error after all catches.
-+        //results_reporter::make_report();
-+
-+        if (!runtime_config::no_result_code()) {
-+            result = results_collector.results( framework::master_test_suite().p_id ).result_code();
-+            if (!NCBI_NS_NCBI::s_GetTestApp().HasTestErrors()
-+                &&  NCBI_NS_NCBI::s_GetTestApp().HasTestTimeouts())
-+            {
-+                // This should certainly go to the output. So we can use only
-+                // printf, nothing else.
-+                printf("There were no test failures, only timeouts.\n"
-+                       " (for autobuild scripts: NCBI_UNITTEST_TIMEOUTS_BUT_NO_ERRORS)\n");
-+            }
-+        }
-+    }
-+#if BOOST_VERSION >= 104200
-+    catch( framework::nothing_to_test const& ) {
-+        result = boost::exit_success;
-+    }
-+#endif
-+    catch( framework::internal_error const& ex ) {
-+        results_reporter::get_stream() << "Boost.Test framework internal error: " << ex.what() << std::endl;
-+        
-+        result = boost::exit_exception_failure;
-+    }
-+    catch( framework::setup_error const& ex ) {
-+        results_reporter::get_stream() << "Test setup error: " << ex.what() << std::endl;
-+        
-+        result = boost::exit_exception_failure;
-+    }
-+    catch( std::exception const& ex ) {
-+        results_reporter::get_stream() << "Test framework error: " << ex.what() << std::endl;
-+
-+        result = boost::exit_exception_failure;
-+    }
-+    catch( ... ) {
-+        results_reporter::get_stream() << "Boost.Test framework internal error: unknown reason" << std::endl;
-+        
-+        result = boost::exit_exception_failure;
-+    }
-+
-+    results_reporter::make_report();
-+
-+    return result;
-+}
-diff --git a/c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp b/c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp
-index 92e817f..cfab8ab 100644
---- a/c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp
-+++ b/c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp
-@@ -1199,7 +1199,7 @@ private:
-     CSeqDBAtlasHolder m_AtlasHolder;
-     
-     /// Reference to memory management layer.
--    mutable CSeqDBAtlas & m_Atlas;
-+    CSeqDBAtlas & m_Atlas;
-     
-     /// The list of database names provided to the constructor.
-     string m_DBNames;
-diff --git a/c++/src/serial/stdtypes.cpp b/c++/src/serial/stdtypes.cpp
-index f6fa651..d6e8f80 100644
---- a/c++/src/serial/stdtypes.cpp
-+++ b/c++/src/serial/stdtypes.cpp
-@@ -720,7 +720,7 @@ public:
-             if ( IsSigned() ) {
-                 // signed -> unsigned
-                 // check for negative value
--                if ( IsNegative(value) )
-+                if ( CParent::IsNegative(value) )
-                     ThrowIntegerOverflow();
-             }
-             if ( sizeof(value) > sizeof(result) ) {
-@@ -751,7 +751,7 @@ public:
-                 // unsigned -> signed
-                 if ( sizeof(value) == sizeof(result) ) {
-                     // same size - check for sign change only
--                    if ( IsNegative(result) )
-+                    if ( CParent::IsNegative(result) )
-                         ThrowIntegerOverflow();
-                 }
-             }
-@@ -786,7 +786,7 @@ public:
-             if ( IsSigned() ) {
-                 // signed -> unsigned
-                 // check for negative value
--                if ( IsNegative(value) )
-+                if ( CParent::IsNegative(value) )
-                     ThrowIntegerOverflow();
-             }
-             if ( sizeof(value) > sizeof(result) ) {
-@@ -817,7 +817,7 @@ public:
-                 // unsigned -> signed
-                 if ( sizeof(value) == sizeof(result) ) {
-                     // same size - check for sign change only
--                    if ( IsNegative(result) )
-+                    if ( CParent::IsNegative(result) )
-                         ThrowIntegerOverflow();
-                 }
-             }
diff --git a/sci-biology/rmblast/rmblast-1.2-r1.ebuild b/sci-biology/rmblast/rmblast-1.2-r1.ebuild
index db7c5a246910..72c740fd30e3 100644
--- a/sci-biology/rmblast/rmblast-1.2-r1.ebuild
+++ b/sci-biology/rmblast/rmblast-1.2-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -9,7 +9,8 @@ MY_NCBI_BLAST_V=2.2.23+
 
 DESCRIPTION="RepeatMasker compatible version of NCBI BLAST+"
 HOMEPAGE="http://www.repeatmasker.org/RMBlast.html"
-SRC_URI="http://www.repeatmasker.org/rmblast-${PV}-ncbi-blast-${MY_NCBI_BLAST_V}-src.tar.gz"
+SRC_URI="http://www.repeatmasker.org/rmblast-${PV}-ncbi-blast-${MY_NCBI_BLAST_V}-src.tar.gz
+	https://dev.gentoo.org/~mgorny/dist/${P}-gcc47.patch.bz2"
 
 LICENSE="OSL-2.1"
 SLOT="0"
@@ -30,7 +31,7 @@ src_prepare() {
 		-e "/DEF_FAST_FLAGS=/s:=\".*\":=\"${CFLAGS}\":g" \
 		-e 's/2.95\* | 2.96\* | 3\.\* | 4\.\* )/2.95\* | 2.96\* | \[3-9\]\.\* )/g' \
 		-i src/build-system/configure || die
-	epatch "${FILESDIR}"/${P}-gcc47.patch
+	epatch "${WORKDIR}"/${P}-gcc47.patch
 }
 
 src_configure() {
diff --git a/sci-biology/vaal/Manifest b/sci-biology/vaal/Manifest
index c1fad41386df..421d21304566 100644
--- a/sci-biology/vaal/Manifest
+++ b/sci-biology/vaal/Manifest
@@ -1,5 +1,5 @@
-AUX vaal-46233_remove-namespace-std.patch 23667 BLAKE2B 1bb17133778df78969b7d5f84e05e2cb8aee9bde2205b1342a6bb6c551955ea4362b5a2d031d2b9b44879c5f343fdc5aa390a159ecf4c3c1c45387c9954ab66b SHA512 47df9a497541d18d96ec6314288e8a429c1d71030f61f8bc29f1a95292f1f2bf53aedd88a16666c204f3bea051b7521ca13de6d03f52f78fcbc5d1cf24a76c47
-DIST VAAL_manual.doc 48128 SHA256 08b662105e8db41b33ea5d6626b58d5a5d793b1dd40fdc663a7068d9abacdc83 SHA512 4da21b6559659764e108c118773bd8ed365b67e3a22de52c7c13429979bb765e7f5d05955ce746a7a55e8d3a6baa752ad575289e71dfd7fb5b8b7207f5cff171 WHIRLPOOL 3a7432974921946e28cd037e47b79fd31631f7a7915a96589a8485b84a3296e1e7d8768e84f4f9086b2648e270f9f84f1e73261bb0b492b3fa7a6cc6fe36f175
-DIST vaal-46233.tar.gz 1148052 SHA256 a1c27ae25583c1333c5169bb33a37cf461bc93b1c18c7e49f585c1cdc9e5a131 SHA512 7a6927d06e1788411063d38e446b7e3c93192e4322a33ea652855f72e550f35debcdb970b895f1fb8504411a54d9096f3dcf506faebd33d50eb033937e15a321 WHIRLPOOL e848bcd6b2dd0c0c52142a3d55acef6a98b816e37355d22386bf3a2fac21e1318a821a394ebd5851cd530aa9afb0d178debc3f74638ee0d0820209a0f432f59f
-EBUILD vaal-46233-r2.ebuild 914 BLAKE2B e66a7c615dd8061306b9f298b51ae7be56eda58109f1f61dde76ef81dcb55571a3a8577347d127e6bc94d2801f796e24970bb09fb390d090763869fd9c64de2d SHA512 134814f2f2c6fe73a6bf31eb466b8f1736d583cf92518382a7e0e0e1b04620b4f8ce6680871b3c2a53e018e25912724113755aac46a1cc14d13b575477768844
+DIST VAAL_manual.doc 48128 BLAKE2B cc31bcdfd4d6faa8c247a9d23a6254ac8a8f8f5de20f8d188c7ed57b9f8231920b4fc7e246394b1bb48ebf457a777d82e704b51b91feb6191e5da331e5765aa9 SHA512 4da21b6559659764e108c118773bd8ed365b67e3a22de52c7c13429979bb765e7f5d05955ce746a7a55e8d3a6baa752ad575289e71dfd7fb5b8b7207f5cff171
+DIST vaal-46233.tar.gz 1148052 BLAKE2B c3fa8ebd722e41bfa1e821d988316900a07d502b6a6b2be394b7227f269ae60a47645b45b6616a782189dcef8a1ea341265e40f257d2ee3f005e8d023273e0b6 SHA512 7a6927d06e1788411063d38e446b7e3c93192e4322a33ea652855f72e550f35debcdb970b895f1fb8504411a54d9096f3dcf506faebd33d50eb033937e15a321
+DIST vaal-46233_remove-namespace-std.patch.bz2 5879 BLAKE2B eb10f5cec8c65c12461346b151dc2c6d60a6f980cdfda78bd97bf0cc33451f808481763e5766b76a78d3d8ef6d5f2f8798bf7b8a7b605e0d32867fdaa9073e3a SHA512 4141094b68b4f9c643abf15d2c5e1486525a69b9d8762cd8034abd3e6f85726ed50d7f25edfcf88fc429ab90db288a583f14b2b5d8e6605cdbfab515f295979c
+EBUILD vaal-46233-r2.ebuild 986 BLAKE2B 703e04878ae3c751725bb6f34bf836602092fd6a3837117973f6203ea1cd63d2aec5f839aba976d9603da3e1294dc310662d99b97eb6b43fa251fb9062fee89e SHA512 b80dd1c52fdb602767af07fbacfbeec949fec5255b93c74007713cbea0a60a184d00d8c1aa762a17d8ac9ddfc746c5ab0c8798d6ea3c8bf9fb78256224685c38
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/vaal/files/vaal-46233_remove-namespace-std.patch b/sci-biology/vaal/files/vaal-46233_remove-namespace-std.patch
deleted file mode 100644
index c3c3ec032481..000000000000
--- a/sci-biology/vaal/files/vaal-46233_remove-namespace-std.patch
+++ /dev/null
@@ -1,911 +0,0 @@
-Remove 'using namespace std' causing massive havoc with newly
-introduced std::align in GCC-5. Fix bug
-https://bugs.gentoo.org/show_bug.cgi?id=568438
-
---- vaal-46233/src/efasta/EfastaTools.cc
-+++ vaal-46233/src/efasta/EfastaTools.cc
-@@ -18,6 +18,8 @@
- #include "math/Functions.h"
- #include "math/Array.h"
- 
-+using std::set;
-+
- #define Err(message)                                      \
- {    cout << message << endl << "\nInvalid.\n" << endl;   \
-      TracebackThisProcess( );    }
---- vaal-46233/src/Equiv.cc
-+++ vaal-46233/src/Equiv.cc
-@@ -9,6 +9,8 @@
- #include "Equiv.h"
- #include "Vec.h"
- 
-+using std::swap;
-+
- bool equivalence_relation::equiv(int a, int b) const
- {    if ( a == b ) return true;
-      int c = a;
---- vaal-46233/src/FastaFilestream.cc
-+++ vaal-46233/src/FastaFilestream.cc
-@@ -13,6 +13,8 @@
- 
- #include <strstream>
- 
-+using std::string;
-+
- template <typename vecT, typename seqT, typename convT, typename verifT>
- FastaFilestream<vecT,seqT,convT,verifT>::FastaFilestream( const String& filename,
-                                                           FastaNameParser* name_parser )
---- vaal-46233/src/FastaFilestreamPreview.cc
-+++ vaal-46233/src/FastaFilestreamPreview.cc
-@@ -11,6 +11,8 @@
- 
- #include <algorithm>
- 
-+using std::streamoff;
-+
- FastaFilestreamPreview::FastaFilestreamPreview(istream& filestream)
-   : max_sequence_size_(0), start_offset_(0)
- {
---- vaal-46233/src/FastaFilestreamPreview.h
-+++ vaal-46233/src/FastaFilestreamPreview.h
-@@ -12,6 +12,8 @@
- 
- #include "Vec.h"
- 
-+using std::streampos;
-+
- // FastaFilestreamPreview understands just enough about the fasta
- // format to be able to count the number of sequences in the specified
- // filestream and to know where each sequence starts in that filestream.
---- vaal-46233/src/Fastavector.cc
-+++ vaal-46233/src/Fastavector.cc
-@@ -14,6 +14,8 @@
- #include <istream>
- #include <string>
- 
-+using std::max;
-+
- // Split this into chunks, separated by gaps ('n'), and return each chunk as a
- // gapless fastavector.
- // TODO: generalize this into a templatized STL algorithm.
---- vaal-46233/src/Fastavector.h
-+++ vaal-46233/src/Fastavector.h
-@@ -24,6 +24,9 @@
- #include <iostream>
- #include <unistd.h>
- 
-+using std::string;
-+using std::istringstream;
-+
- typedef std::tuple<String, int, int> FastaRegion;
- 
- class fastaindex {
---- vaal-46233/src/FetchReads.cc
-+++ vaal-46233/src/FetchReads.cc
-@@ -36,6 +36,8 @@
- #include "Qualvector.h"
- #include "random/Random.h"
- 
-+using std::istringstream;
-+
- // Heuristic constants:
- 
- namespace
---- vaal-46233/src/feudal/BaseVec.cc
-+++ vaal-46233/src/feudal/BaseVec.cc
-@@ -21,6 +21,7 @@
- using std::ostream;
- using std::cout;
- using std::endl;
-+using std::max_element;
- 
- // Cap: in a given basevector, replace any sequence of N > n identical
- // bases by n of the same base.
---- vaal-46233/src/graph/Digraph.cc
-+++ vaal-46233/src/graph/Digraph.cc
-@@ -16,6 +16,8 @@
- #include "graph/Digraph.h"
- #include "math/Functions.h"
- 
-+using std::make_pair;
-+
- Bool digraph::HasEdge( int v, int w ) const {
-   return find( from_[v].begin(),  from_[v].end(), w ) != from_[v].end();
- }
---- vaal-46233/src/graph/DigraphTemplate.h
-+++ vaal-46233/src/graph/DigraphTemplate.h
-@@ -34,6 +34,8 @@
- #include "graph/Digraph.h"
- #include <cstddef>
- 
-+using std::make_pair;
-+
- template<class E> vec<int> digraphE<E>::EdgesConnectedTo( const vec<int>& v ) const
- {    vec<int> G = VerticesConnectedTo(v), e;
-      for ( int x = 0; x < G.isize( ); x++ )
---- vaal-46233/src/IndexedAlignmentPlusVector.cc
-+++ vaal-46233/src/IndexedAlignmentPlusVector.cc
-@@ -9,6 +9,8 @@
- #include "IndexedAlignmentPlusVector.h"
- #include "VecAlignmentPlus.h"
- 
-+using std::streamoff;
-+
- // These strings are at the head of the vector and index files for verification purposes.
- 
- const String VecAlignmentPlusHeaderIO::mStrVectorHeader( "alignment_plus vector V.2\n" );
---- vaal-46233/src/IndexedAlignmentPlusVector.h
-+++ vaal-46233/src/IndexedAlignmentPlusVector.h
-@@ -15,6 +15,7 @@
- 
- #include "Alignment.h"
- 
-+using std::streampos;
- 
- // This class encapsulates the header information for both vectors and indices.
- 
---- vaal-46233/src/kmers/kmer_parcels/KmerParcelsBuilder.cc
-+++ vaal-46233/src/kmers/kmer_parcels/KmerParcelsBuilder.cc
-@@ -10,6 +10,7 @@
- #include "kmers/KmerParcels.h"
- #include "system/WorklistN.h"
- 
-+using std::fixed;
- 
- inline String Tag(String S = "KPs") { return Date() + " (" + S + "): "; } 
- 
---- vaal-46233/src/kmers/kmer_parcels/KmerParcelsClasses.h
-+++ vaal-46233/src/kmers/kmer_parcels/KmerParcelsClasses.h
-@@ -6,6 +6,9 @@
- //   Institute is not responsible for its use, misuse, or functionality.     //
- ///////////////////////////////////////////////////////////////////////////////
- 
-+using std::hex;
-+using std::dec;
-+
- // ---------------------------------
- // NaifTimer
- // ---------------------------------
---- vaal-46233/src/kmers/kmer_parcels/KmerParcelsStatistics.h
-+++ vaal-46233/src/kmers/kmer_parcels/KmerParcelsStatistics.h
-@@ -10,7 +10,7 @@
- #ifndef KMERS__KMER_PARCELS__KMER_PARCELS_STATISTICS_H
- #define KMERS__KMER_PARCELS__KMER_PARCELS_STATISTICS_H
- 
--
-+using std::map;
- 
- // --------------------------------------
- // MapOfCounters
---- vaal-46233/src/layout/ContigActualloc.h
-+++ vaal-46233/src/layout/ContigActualloc.h
-@@ -17,6 +17,8 @@
- #include "system/Crash.h"
- #include "Misc.h"
- 
-+using std::set;
-+using std::map;
- 
- //
- // Class contig_actualloc
---- vaal-46233/src/lookup/ImperfectLookup.h
-+++ vaal-46233/src/lookup/ImperfectLookup.h
-@@ -52,6 +52,8 @@
- #include "lookup/AlignCollector.h"
- #include "solid/Solid.h"
- 
-+using std::unique_ptr;
-+
- class TaskTimer;
- 
- 
-@@ -534,7 +536,7 @@
-       aligns.resize( nqueries );
-     }
- 
--    auto_ptr<TaskTimer> t1, t2;
-+    unique_ptr<TaskTimer> t1, t2;
- 
-     if ( m_instr_level & IO_TIMER != 0 ) t1.reset( new TaskTimer() );
-     if ( m_instr_level & CPU_TIMER != 0 ) t2.reset( new TaskTimer() );
---- vaal-46233/src/lookup/LookAlign.cc
-+++ vaal-46233/src/lookup/LookAlign.cc
-@@ -29,6 +29,8 @@
- #include "random/Random.h"
- #include "system/ParsedArgs.h"
- 
-+using std::istrstream;
-+
- String QUERY("QUERY");
- 
- void look_align::ResetFromAlign(const align & al, const basevector & b1,
---- vaal-46233/src/lookup/LookAlignFinder.h
-+++ vaal-46233/src/lookup/LookAlignFinder.h
-@@ -12,6 +12,8 @@
- #include "lookup/LookAlign.h"
- #include "Vec.h"
- 
-+using std::set;
-+
- /**
-    Class: LookAlignFinder
- 
---- vaal-46233/src/lookup/LookAlignSort.h
-+++ vaal-46233/src/lookup/LookAlignSort.h
-@@ -15,6 +15,8 @@
- 
- #include <functional>
- 
-+using std::set;
-+
- /// Read in look_aligns from file, sort, and load into vecs
- /// \param fname name of look_align text file
- /// \param aligns vector into which to put the alignments
---- vaal-46233/src/lookup/LookupTable.h
-+++ vaal-46233/src/lookup/LookupTable.h
-@@ -18,6 +18,8 @@
- 
- #include <set>
- 
-+using std::set;
-+
- typedef pair<unsigned int, unsigned int> LocSeq;
- 
- ///
---- vaal-46233/src/lookup/QueryLookupTableCore.cc
-+++ vaal-46233/src/lookup/QueryLookupTableCore.cc
-@@ -456,6 +456,9 @@
- #include "system/ParsedArgs.h"
- #include "system/file/FileReader.h"
- 
-+using std::istrstream;
-+using std::less_equal;
-+
- #define ABORT(MSG)                                 \
- {    out << MSG << "  Abort." << endl << endl;     \
-      exit(1);    }
---- vaal-46233/src/lookup/ShortQueryLookup.cc
-+++ vaal-46233/src/lookup/ShortQueryLookup.cc
-@@ -32,6 +32,8 @@
- #include "lookup/AlignCollector.h"
- #include "lookup/ImperfectLookup.h"
- 
-+using std::ios_base;
-+
- // Run an alignment processing chain: seqs -> look -> receiver -> aligns
- // That is, look turns seqs into hits, which receiver accepts
- // and turns into alignments which are passed to aligns.  The
---- vaal-46233/src/Map.h
-+++ vaal-46233/src/Map.h
-@@ -21,7 +21,7 @@
- #include <map>
- #include <ext/hash_map>
- using namespace __gnu_cxx;
--
-+using std::map;
- 
- ///Return true if k is a key in map m
- template<class Key, class Value, typename Cmp> 
---- vaal-46233/src/math/Array.h
-+++ vaal-46233/src/math/Array.h
-@@ -12,6 +12,9 @@
- #include "CoreTools.h"
- #include "Vec.h"
- 
-+using std::map;
-+using std::fill;
-+
- // ==============================================================================
- // A fixed-size simple c-style 2D array that allocates faster than vec< vec<T> >
- // The elements are uninitialized.
---- vaal-46233/src/math/Functions.cc
-+++ vaal-46233/src/math/Functions.cc
-@@ -10,8 +10,8 @@
- #include "STLExtensions.h"
- #include "math/Functions.h"
- 
--
--
-+using std::isfinite;
-+using std::make_pair;
- 
- /*  CombineNormalDistribution              Filipe Ribeiro 2009-06-22
-  *
---- vaal-46233/src/math/Functions.h
-+++ vaal-46233/src/math/Functions.h
-@@ -14,6 +14,10 @@
- #include <cmath>
- #include <numeric>
- 
-+using std::min;
-+using std::cerr;
-+using std::swap;
-+
- // ===========================================================================
- //
- // Min functions
---- vaal-46233/src/math/HoInterval.cc
-+++ vaal-46233/src/math/HoInterval.cc
-@@ -10,6 +10,8 @@
- #include "math/HoInterval.h"
- #include "STLExtensions.h"
- 
-+using std::make_pair;
-+
- bool ho_interval::Merge(const ho_interval & o) {
-   if (!Meets(*this,o)) return false;
-   *this = Span(*this, o);
---- vaal-46233/src/math/HoInterval.h
-+++ vaal-46233/src/math/HoInterval.h
-@@ -14,6 +14,8 @@
- #include "feudal/MasterVec.h"
- #include "feudal/SerfVec.h"
- 
-+using std::max;
-+
- /// Class: ho_interval
- /// A half-open interval [a, b).
- class ho_interval {
---- vaal-46233/src/PackAlign.h
-+++ vaal-46233/src/PackAlign.h
-@@ -133,6 +133,8 @@
- #include "pairwise_aligners/Mutmer.h"
- #include "feudal/BinaryStream.h"
- 
-+using std::make_pair;
-+
- const int Bits2  = 3, Bits3  = 7, Bits4 = 15, Bits10 = 1023, Bits12 = 4095, 
-   Bits16 = 65535;
- 
---- vaal-46233/src/pairwise_aligners/MakeAlignsMethod.cc
-+++ vaal-46233/src/pairwise_aligners/MakeAlignsMethod.cc
-@@ -19,6 +19,9 @@
- #include "pairwise_aligners/AlignFromMutmers.h"
- #include "pairwise_aligners/SmithWatBandedA.h"
- 
-+using std::map;
-+using std::set;
-+
- // If there's a perfect match of length at least perf but we produced no proper 
- // alignment, use banded Smith-Waterman to create one.
- 
---- vaal-46233/src/pairwise_aligners/MatchList.cc
-+++ vaal-46233/src/pairwise_aligners/MatchList.cc
-@@ -9,6 +9,8 @@
- 
- #include "pairwise_aligners/MatchList.h"
- 
-+using std::max;
-+
- bool MatchList::FindMatchInSorted( const int id1, const Match& newMatch ) const 
- {
-   const vec<Match>& sortedMatches = m_sortedMatches[id1];
---- vaal-46233/src/pairwise_aligners/SuffixTree.h
-+++ vaal-46233/src/pairwise_aligners/SuffixTree.h
-@@ -23,6 +23,8 @@
- #include <list>
- #include <string>
- 
-+using std::list;
-+
- /**
-  * Implementation of a suffix tree for basevectors.
-  * This is a data structure for exact (sub)string matching.
---- vaal-46233/src/paths/AlignHyperKmerPath.cc
-+++ vaal-46233/src/paths/AlignHyperKmerPath.cc
-@@ -23,6 +23,9 @@
- #include "paths/KmerBaseBroker.h"
- #include "paths/KmerPath.h"
- 
-+using std::ostringstream;
-+using std::set;
-+
- // Function: AlignHyperKmerPath
- //
- // AlignHyperKmerPath takes a HyperKmerPath h, whose KmerPath edges are assumed
---- vaal-46233/src/paths/AlignSeqsToHyper.cc
-+++ vaal-46233/src/paths/AlignSeqsToHyper.cc
-@@ -26,6 +26,7 @@
- #include "paths/ReadsToPathsCoreX.h"
- #include "paths/SeqOnHyper.h"
- 
-+using std::multimap;
- 
- // Local class: simple_align
- //
---- vaal-46233/src/paths/HyperKmerPath.cc
-+++ vaal-46233/src/paths/HyperKmerPath.cc
-@@ -19,6 +19,8 @@
- #include "paths/HyperKmerPath.h"
- #include "paths/KmerBaseBroker.h"
- 
-+using std::ostrstream;
-+using std::ends;
- 
- void HyperKmerPath::ReduceLoops( )
- {    for ( int v = 0; v < N( ); v++ )
---- vaal-46233/src/paths/KmerBaseBroker.h
-+++ vaal-46233/src/paths/KmerBaseBroker.h
-@@ -20,6 +20,8 @@
- #include <algorithm>  // for set_union
- #include <map>
- 
-+using std::map;
-+
- /**
-    Class: KmerBaseBrokerTemplate
- 
---- vaal-46233/src/paths/KmerPath.h
-+++ vaal-46233/src/paths/KmerPath.h
-@@ -22,6 +22,8 @@
- #include "HashSimple.h"
- #include "graph/Digraph.h"
- 
-+using std::make_pair;
-+
- class KmerPathLoc;  // forward declaration
- 
- /**
---- vaal-46233/src/paths/KmerPathInterval.h
-+++ vaal-46233/src/paths/KmerPathInterval.h
-@@ -8,6 +8,8 @@
- #include "CommonSemanticTypes.h"
- #include "feudal/BinaryStreamTraits.h"
- 
-+using std::max;
-+
- // Portability note: endianness
- // The implementations here would need to be changed for big endian architectures.
- 
-@@ -285,6 +287,12 @@
-    Models <tagged read path interval>.
- */
- // TODO: potentially dangerous truncation of index by PathId, ReadId
-+template<class TAG>
-+void Contains( const vec<TAG>& segs, kmer_id_t index, vec<longlong>& answer, bool append = false, int cap = -1 );
-+
-+template<class TAG>
-+void Contains( const vec<TAG>& segs, KmerPathInterval rpi, vec<longlong>& answer, bool append = false, int cap = -1 );
-+
- class tagged_rpint {
- 
-      public: /* PUBLIC METHODS */
-@@ -362,11 +370,11 @@
- 
-      template<class TAG>
-      friend void Contains( const vec<TAG>& segs, kmer_id_t index,
--          vec<longlong>& answer, bool append = false, int cap = -1 );
-+          vec<longlong>& answer, bool append, int cap );
- 
-      template<class TAG>
-      friend void Contains( const vec<TAG>& segs, KmerPathInterval rpi,
--          vec<longlong>& answer, bool append = false, int cap = -1 );
-+          vec<longlong>& answer, bool append, int cap );
- 
-      template<class TAG>
-      friend longlong Instance( const vec<TAG>& segs, kmer_id_t k );
-@@ -489,11 +497,11 @@
- 
-      template<class TAG>
-      friend void Contains( const vec<TAG>& segs, kmer_id_t index,
--          vec<longlong>& answer, bool append = false, int cap = -1 );
-+          vec<longlong>& answer, bool append, int cap );
- 
-      template<class TAG>
-      friend void Contains( const vec<TAG>& segs, KmerPathInterval rpi,
--          vec<longlong>& answer, bool append = false, int cap = -1 );
-+          vec<longlong>& answer, bool append, int cap );
- 
-      template<class TAG>
-      friend longlong Instance( const vec<TAG>& segs, kmer_id_t k );
-@@ -620,11 +628,11 @@
- 
-      template<class TAG>
-      friend void Contains( const vec<TAG>& segs, kmer_id_t index,
--          vec<longlong>& answer, bool append = false, int cap = -1 );
-+          vec<longlong>& answer, bool append, int cap );
- 
-      template<class TAG>
-      friend void Contains( const vec<TAG>& segs, KmerPathInterval rpi,
--          vec<longlong>& answer, bool append = false, int cap = -1 );
-+          vec<longlong>& answer, bool append, int cap );
- 
-      template<class TAG>
-      friend kmer_id_t Instance( const vec<TAG>& segs, kmer_id_t k );
---- vaal-46233/src/paths/ReadsToPathsCoreX.cc
-+++ vaal-46233/src/paths/ReadsToPathsCoreX.cc
-@@ -20,6 +20,8 @@
- #include "paths/MakeAlignsPathsParallelX.h"
- #include "paths/ReadsToPathsCoreX.h"
- 
-+using std::map;
-+
- static inline 
- String Tag(String S = "RTPCX") { return Date() + " (" + S + "): "; } 
- 
---- vaal-46233/src/paths/SuperBaseVector.h
-+++ vaal-46233/src/paths/SuperBaseVector.h
-@@ -10,6 +10,8 @@
- #include <numeric>
- #include <functional>
- 
-+using std::mem_fun_ref;
-+
- /// A simple class which holds a series of basevectors with
- /// (possibly negative) gaps between them.  This is what a 
- /// KmerPath logically maps to in sequence space.  The function
---- vaal-46233/src/polymorphism/VAAL2.cc
-+++ vaal-46233/src/polymorphism/VAAL2.cc
-@@ -42,7 +42,7 @@
- #include "feudal/BinaryStream.h"
- #include "feudal/VirtualMasterVec.h"
- 
--using namespace std;
-+
- 
- // Trim reads so that they contain only kmers in the unipaths.
- 
---- vaal-46233/src/polymorphism/VAAL3.cc
-+++ vaal-46233/src/polymorphism/VAAL3.cc
-@@ -29,6 +29,8 @@
- #include "polymorphism/VAALTools.h"
- #include "solexa/SolexaTools.h"
- 
-+using std::ostringstream;
-+
- int main( int argc, char *argv[] )
- {
-      RunTime( );
---- vaal-46233/src/PrintAlignment.h
-+++ vaal-46233/src/PrintAlignment.h
-@@ -14,6 +14,8 @@
- #include "CoreTools.h"
- #include "Qualvector.h"
- 
-+using std::ostringstream;
-+
- void PrintBlanks( ostream& out, int n );
- 
- template<class BASEVEC>
---- vaal-46233/src/Qualvector.cc
-+++ vaal-46233/src/Qualvector.cc
-@@ -10,6 +10,8 @@
- #include "FastIfstream.h"
- #include "Qualvector.h"
- 
-+using std::istrstream;
-+
- /// \file
- /// \ingroup grp_quals
- /// \copydoc Qualvector.h
---- vaal-46233/src/SeqInterval.cc
-+++ vaal-46233/src/SeqInterval.cc
-@@ -9,6 +9,8 @@
- #include "SeqInterval.h"
- #include "Vec.h"
- 
-+using std::max;
-+using std::min;
- 
- /*
-  * seq_interval
---- vaal-46233/src/SeqInterval.h
-+++ vaal-46233/src/SeqInterval.h
-@@ -14,7 +14,9 @@
- #include <algorithm>
- #include <iostream>
- 
--using namespace std;
-+using std::binary_function;
-+using std::ostream;
-+using std::istream;
- 
- /*
-  * class seq_interval
---- vaal-46233/src/Set.h
-+++ vaal-46233/src/Set.h
-@@ -16,7 +16,7 @@
- #include <set>
- #include "CoreTools.h"
- 
--using namespace std;
-+using std::set;
- 
- template<class T> bool Member( const set<T>& the_set, const T& value )
- {    return the_set.find(value) != the_set.end( );    }  // Breaks cxx 
---- vaal-46233/src/ShortVector.h
-+++ vaal-46233/src/ShortVector.h
-@@ -14,6 +14,8 @@
- #include "system/Types.h"
- #include "feudal/BinaryStream.h"
- 
-+using std::uninitialized_fill_n;
-+
- // ================================================================================
- //
- // A shortvector holds a list of up to 255 things of any type T.  
---- vaal-46233/src/solexa/FourBase2.h
-+++ vaal-46233/src/solexa/FourBase2.h
-@@ -15,6 +15,10 @@
- #include "feudal/MasterVec.h"
- #include "feudal/SerfVec.h"
- 
-+using std::max_element;
-+using std::min_element;
-+using std::accumulate;
-+
- class four_base2 {
- 
- public:
---- vaal-46233/src/solexa/FourBase.cc
-+++ vaal-46233/src/solexa/FourBase.cc
-@@ -9,6 +9,9 @@
- 
- #include "solexa/FourBase.h"
- 
-+using std::string;
-+using std::istringstream;
-+
- int four_base::Call( ) const
- {
-     int result = 0;
---- vaal-46233/src/solexa/FourBase.h
-+++ vaal-46233/src/solexa/FourBase.h
-@@ -16,6 +16,8 @@
- #include "feudal/MasterVec.h"
- #include "feudal/SerfVec.h"
- 
-+using std::max;
-+
- /*
-    Class: four_base
- 
---- vaal-46233/src/solexa/SolexaMetrics.h
-+++ vaal-46233/src/solexa/SolexaMetrics.h
-@@ -42,6 +42,8 @@
- #include "CommonSemanticTypes.h"
- #include <map>
- 
-+using std::map;
-+
- /// Definition of general macros.
- 
- class solexa_metric_db {
---- vaal-46233/src/solexa/SolexaTools.cc
-+++ vaal-46233/src/solexa/SolexaTools.cc
-@@ -20,6 +20,8 @@
- #include "FastaFileset.h"
- #include "util/BaitMap.h"
- 
-+using std::ostringstream;
-+
- void SolexaPredictorParameters::SetFromFile(const String & fname) {
-   Ifstream(is, fname);
-   String params = Slurp(is);
---- vaal-46233/src/STLExtensions.h
-+++ vaal-46233/src/STLExtensions.h
-@@ -9,7 +9,7 @@
- #ifndef STLEXTENSIONS_H
- #define STLEXTENSIONS_H
- 
--using namespace std;
-+
- 
- #include <functional>
- #include <vector>
-@@ -21,6 +21,13 @@
- #include "feudal/BinaryStream.h"
- #include "system/StaticAssert.h"
- 
-+using std::binary_function;
-+using std::unary_function;
-+using std::pair;
-+using std::bitset;
-+using std::vector;
-+using std::ostream;
-+
- /// minimum<T> is a function object.  
- ///
- /// If f is an object of class minimum<T> and x and y are objects of
---- vaal-46233/src/system/ParsedArgs.cc
-+++ vaal-46233/src/system/ParsedArgs.cc
-@@ -26,6 +26,9 @@
- #include "system/HostName.h"
- #include "system/UseGDB.h"
- 
-+using std::istrstream;
-+using std::mem_fun_ref;
-+
- #ifndef FatalErr
-      #define FatalErr(message) { cout << message << endl << endl; exit(-1); }
- #endif
---- vaal-46233/src/system/ParsedArgs.h
-+++ vaal-46233/src/system/ParsedArgs.h
-@@ -97,6 +97,8 @@
- #include "TokenizeString.h"
- #include "ParseSet.h"
- 
-+using std::stringstream;
-+
- class parsed_arg_help {
- 
-  public:
---- vaal-46233/src/system/ProcBuf.cc
-+++ vaal-46233/src/system/ProcBuf.cc
-@@ -15,6 +15,8 @@
- #include <sys/wait.h>
- #include <unistd.h>
- 
-+using std::ios_base;
-+
- namespace
- {
- size_t const BUFFER_SIZE = 8192;
---- vaal-46233/src/system/RunTime.cc
-+++ vaal-46233/src/system/RunTime.cc
-@@ -41,6 +41,10 @@
-      #include <unwind.h>
- #endif
- 
-+using std::strstream;
-+using std::hex;
-+using std::setw;
-+
- /// ===========================================================================
- ///
- /// ReturnAddress(i), where 0 <= i <= 100: get the return address.  The
---- vaal-46233/src/system/RunTime.h
-+++ vaal-46233/src/system/RunTime.h
-@@ -14,6 +14,8 @@
- #include "system/Exit.h"
- #include "system/Types.h"
- 
-+using std::ostream;
-+
- typedef void ArachneSignalHandler(int, siginfo_t*, void*);
- 
- void arachne_signal_handler( int signal_number, siginfo_t* info, void* context,
---- vaal-46233/src/system/System.cc
-+++ vaal-46233/src/system/System.cc
-@@ -35,6 +35,11 @@
- 
- #include <dirent.h>
- 
-+using std::istringstream;
-+using std::istream_iterator;
-+using std::ostrstream;
-+using std::ends;
-+
- int SystemInternal( String command, const char *shell )
- {
-   flush(cout);
---- vaal-46233/src/system/System.h
-+++ vaal-46233/src/system/System.h
-@@ -21,6 +21,17 @@
- #include "system/Exit.h"
- #include "system/file/TempFile.h"
- 
-+using std::vector;
-+using std::ostream;
-+using std::ofstream;
-+using std::cout;
-+using std::flush;
-+using std::endl;
-+using std::istream;
-+using std::ifstream;
-+using std::ios;
-+using std::setprecision;
-+
- #ifndef InputErr
-      #define InputErr(message)                                               \
-      {    cout << "\nFatal error at " << Date( ) << ": " << message << endl; \
---- vaal-46233/src/system/TraceVal.h
-+++ vaal-46233/src/system/TraceVal.h
-@@ -24,6 +24,9 @@
- #include "system/Types.h"
- #include "system/Assert.h"
- 
-+using std::cout;
-+using std::endl;
-+
- // Macros: Tracing macros
- //   TRACEVAL_ON - undefine if you're not doing tracing
- //   TRACEVAL_STOP_TRACING_COPIES -- call before an operation that shuffles
---- vaal-46233/src/system/Types.h
-+++ vaal-46233/src/system/Types.h
-@@ -14,7 +14,7 @@
- #include <cstdlib>
- #include <netinet/in.h>
- 
--using namespace std;
-+
- 
- // This assumes that all suns run Solaris...
- #if __sun == 1
---- vaal-46233/src/util/BaitMap.cc
-+++ vaal-46233/src/util/BaitMap.cc
-@@ -236,7 +236,7 @@
- bool BaitMap::write(String file_name)
- {
-     std::ofstream out(file_name.c_str());
--    ForceAssert(out);
-+    ForceAssert(static_cast<bool>(out));
- 
-     for (unsigned int i = 0; i < this->size(); i++)
-     {
-@@ -250,7 +250,7 @@
-     }
- 
-     out.close();
--    ForceAssert(out);
-+    ForceAssert(static_cast<bool>(out));
- 
-     return true;
- }
-@@ -260,7 +260,7 @@
- bool BaitMap::write_names(String file_name)
- {
-     std::ofstream out(file_name.c_str());
--    ForceAssert(out);
-+    ForceAssert(static_cast<bool>(out));
- 
-     for (unsigned int i = 0; i < this->size(); i++)
-     {
-@@ -268,7 +268,7 @@
-     }
- 
-     out.close();
--    ForceAssert(out);
-+    ForceAssert(static_cast<bool>(out));
- 
-     return true;
- }
---- vaal-46233/src/util/BaitMap.h
-+++ vaal-46233/src/util/BaitMap.h
-@@ -20,6 +20,8 @@
- 
- #include <map>
- 
-+using std::map;
-+
- class BaitMap
- {
- public:
---- vaal-46233/src/util/Qualb.cc
-+++ vaal-46233/src/util/Qualb.cc
-@@ -10,6 +10,8 @@
- #include "FastIfstream.h"
- #include "Qualvector.h"
- 
-+using std::istrstream;
-+
- int main( int argc, char *argv[] )
- {
-      RunTime( );
---- vaal-46233/src/Vec.h
-+++ vaal-46233/src/Vec.h
-@@ -48,6 +48,14 @@
- #include "Compare.h"
- #include "system/file/FileReader.h"
- 
-+using std::initializer_list;
-+using std::numeric_limits;
-+using std::ostream_iterator;
-+using std::less;
-+using std::equal_to;
-+using std::setfill;
-+using std::setw;
-+
- /////////////////////////////////////////////////////////////////////////////
- //
- //  vec Class Declaration and Template Definitions
---- vaal-46233/src/VecUtilities.h
-+++ vaal-46233/src/VecUtilities.h
-@@ -37,6 +37,7 @@
- #include "Vec.h"
- #include <cstddef>
- 
-+using std::greater;
- 
- /////////////////////////////////////////////////////////////////////////////
- //
diff --git a/sci-biology/vaal/vaal-46233-r2.ebuild b/sci-biology/vaal/vaal-46233-r2.ebuild
index 7185fc1c24df..85076f330579 100644
--- a/sci-biology/vaal/vaal-46233-r2.ebuild
+++ b/sci-biology/vaal/vaal-46233-r2.ebuild
@@ -9,7 +9,8 @@ DESCRIPTION="Algorithm for detecting SNPs, indels, and other polymorphisms"
 HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd/"
 SRC_URI="
 	ftp://ftp.broad.mit.edu/pub/crd/VAAL/latest_source_code/${P}.tar.gz
-	ftp://ftp.broad.mit.edu/pub/crd/VAAL/VAAL_manual.doc"
+	ftp://ftp.broad.mit.edu/pub/crd/VAAL/VAAL_manual.doc
+	https://dev.gentoo.org/~mgorny/dist/${P}_remove-namespace-std.patch.bz2"
 
 LICENSE="Whitehead-MIT"
 SLOT="0"
@@ -25,7 +26,7 @@ DEPEND="
 
 DOCS=( "${DISTDIR}/VAAL_manual.doc" )
 PATCHES=(
-	"${FILESDIR}/${P}_remove-namespace-std.patch"
+	"${WORKDIR}/${P}_remove-namespace-std.patch"
 )
 
 src_prepare() {
diff --git a/sci-biology/wise/Manifest b/sci-biology/wise/Manifest
index e776c86aceee..ba7c4502f898 100644
--- a/sci-biology/wise/Manifest
+++ b/sci-biology/wise/Manifest
@@ -1,7 +1,4 @@
-AUX wise-2.4.0_alpha-cflags.patch 27241 BLAKE2B 940d7e8309fcca65ebd395465d1f82975f86b24cb882bb3e303c40e36cc8322a83efaa38596b10ffea46fbc8765dd91907201bd283f8f2a36ef8de11abda0f24 SHA512 2f4faaff8198c63fb22edde934584fa2d00d2a333c5caefbbbc569e6136546aa274060453f093e0791a4d61bc901e1f199c47bb60d1be9f0ac32b3709cb025ab
-AUX wise-2.4.0_alpha-glibc-2.10.patch 8068 BLAKE2B dd36c52033fa72c14f06b9421392c6d98609206d02c449f18e32dc7d2a8cf213e9edea85c1c58e57ffa9ddd82d19e1bf26f2b21a8a0572640f3a51da0aaa7d6e SHA512 eba50ed8e12ca94d026fed95602ec1d1683ea26f0195952304a1caebdb94df700b547168a6da4a9ad4289dd9c6060572b4ed9dcfcc7698dff2812765adc556e1
-AUX wise-api.tex.patch 2234 BLAKE2B 79bf7d6ea125456de2df26fe2a9198e97b0603baa7b40eb9e70e66186e3b445113b5ebf160bd7c05c83910a07dec55a6cc1d953d98d28a67e97fe46fde20a4f2 SHA512 1cb7b5f5377d4d235707d32d74087598db5abc793b2aba8272a7da941a25d5618691212240eb25c078df39868ea7adfacfba3d218bd77fcea5d57b3b2ef51a0b
-AUX wise-env 40 BLAKE2B 595ad1009800c96dc304f055547b066953ae008958e228e0469e5cff29682051dc5704ba541b152df0a72ac0ea0be0b7bf392c228c6cbbfa9d02ff737c770332 SHA512 58cfa40d4d3b2623df82bb321f8dd2f5ebbee099ccfd4ac0e3eb9edf5693dbaee0581f8986b4923c60060d92c028e731f15c047e18f86efb76adaf4ec386e96c
-DIST wise2.4.0alpha.tar.gz 3296399 SHA256 6ec8be1ea6f0559d8a2659fe9c0626408fa2b3e327cae345d0e48bb971531853 SHA512 a2288d7304e7768328689514a986aeff62a0ca6538ee61177a434fb08065f83ab5db39e0cb9101dd8ae9a91f7d95d05528d7ad23df0c394587717c584bf2341c WHIRLPOOL cb6b34dc7d6b758d83a97af491e803230f8dfbd0d0600600fc4c2513b9450d7b6da988d5d584bf9db6193f938df59899e49f2a4e26d5f29c5e089a741d00f6ec
-EBUILD wise-2.4.0_alpha.ebuild 1629 BLAKE2B bdcd19bfc794df1bf5405ccd604fb68662bc0c22cdfacf039f9de2501708493967e58020e56c3047d189966669ee47f8d2b30ae2db3d059748e0fded38b5fdf3 SHA512 cf1b57b1d14396ed4da12a1f24932a6a6e43a5e4eb61642bc40906eea4dbc57c58c0c4daac29122744b8c54b5f434e5f49d964d3fbc05b60dac6cd02514f2f43
+DIST wise-2.4.0_alpha-patchset.tar.bz2 7244 BLAKE2B 3c921b61e6a30515d790abd8168b5fbc4f8add44f1133cf7d163a98a6935a74ae7c9f79b72874a509bb743aa5b340c92a049ad091380f9cd33b0b9154cca5974 SHA512 ca73f1b03e14cef44d84484c64d06c4856d6ef33b7434de5ac58725cea1d071d875a7b073fc181da33a7490c4f086f674a9a52db4d36e78f4f5b75b28b855cfe
+DIST wise2.4.0alpha.tar.gz 3296399 BLAKE2B a7fbac022c62606ce865250f4091497e9c86331d2d2050fc4f69614aa5e95313eac3a0fcd49451c724c9b50bc6ac63700cd44828736b7a4d15eff2bc21fc29ec SHA512 a2288d7304e7768328689514a986aeff62a0ca6538ee61177a434fb08065f83ab5db39e0cb9101dd8ae9a91f7d95d05528d7ad23df0c394587717c584bf2341c
+EBUILD wise-2.4.0_alpha.ebuild 1740 BLAKE2B bc82688af330de9693862d767503e0c96e17483fd1631be4d60ff7952de8af77cf3ceacdcb35ff081faa39f024fbc11202a92e7992c8fae080650ea51b35596b SHA512 345ff496a93020ad0b219b83b53ee8c21eb287384559573cc7101e976022c78c42322a2f05a1f89acce6af4252e2d544719f2072cf80003beb70a3dc00d0c02d
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/wise/files/wise-2.4.0_alpha-cflags.patch b/sci-biology/wise/files/wise-2.4.0_alpha-cflags.patch
deleted file mode 100644
index d3c17098105e..000000000000
--- a/sci-biology/wise/files/wise-2.4.0_alpha-cflags.patch
+++ /dev/null
@@ -1,407 +0,0 @@
-diff --git a/src/base/makefile b/src/base/makefile
-index 4620f19..a84e2c7 100644
---- a/src/base/makefile
-+++ b/src/base/makefile
-@@ -20,8 +20,8 @@ NBASEOBJ = wiseconfig.o \
- 
- 
- #CFLAGS = -c  -g -DUNIX -DWISE_MEMORY_WATCH
--CFLAGS = -c  -O2 -DUNIX -pthread
--LFLAGS =  -g  -lm 
-+CFLAGS += -c -DUNIX -pthread
-+LFLAGS =  -lm 
- DFLAGS = -n Wise2_ -a _api.h -b _api.t -l -D
- AR_OPTIONS = ru
- 
-diff --git a/src/corba/makefile b/src/corba/makefile
-index df3dd78..237a1ba 100644
---- a/src/corba/makefile
-+++ b/src/corba/makefile
-@@ -1,10 +1,10 @@
- 
- 
--CC = cc
-+CC += gcc
- INCFLAGS = -I../base/ -I../dynlibsrc
- #gCFLAGS = -Wall -g -pedantic -c  -DUNIX -I../base/
--#CFLAGS =  -O2 -c  -DUNIX  -I../base/ `glib-config --cflags` -I/usr/local/include/orbit-1.0/
--CFLAGS =  -pthread -c  -DUNIX  -I../base/ -I../dynlibsrc `orbit-config --cflags client`
-+#CFLAGS =  -O2 -c  -DUNIX  -I../base/ `pkg-config glib-2.0 --cflags` -I/usr/local/include/orbit-1.0/
-+CFLAGS +=  -pthread -c  -DUNIX  -I../base/ -I../dynlibsrc `pkg-config ORBit-2.0 --cflags`
- LFLAGS =   -L../base/ -lm -lpthread
- AR_OPTIONS = ru
- 
-@@ -14,18 +14,18 @@ hspscan_corba.c : hspscan_corba.idl
- 	orbit-idl hspscan_corba.idl
- 
- test_server : test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o 
--	cc -g -o test_server  test_server.o hspscan_server_impl.o  hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o  corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o   ../dynlibsrc/libdyna_glib.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
-+	$(CC) $(CFLAGS) $(LDFLAGS) -o test_server  test_server.o hspscan_server_impl.o  hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o  corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o   ../dynlibsrc/libdyna_glib.a `pkg-config glib-2.0 --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
- 
- scanwise_protein_index : scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o 
--	cc -o scanwise_protein_index  scanwise_protein_index.o hspscan_server_impl.o  hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o  corba_singleton.o  ../dynlibsrc/libdyna_glib.a ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
-+	$(CC) $(CFLAGS) $(LDFLAGS) -o scanwise_protein_index  scanwise_protein_index.o hspscan_server_impl.o  hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o  corba_singleton.o  ../dynlibsrc/libdyna_glib.a ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config glib-2.0 --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
- 
- 
- test_client : test_client.o hspscan_corba-common.o hspscan_corba-stubs.o 
--	cc -g -o test_client  test_client.o  hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
-+	$(CC) $(CFLAGS) $(LDFLAGS) -o test_client  test_client.o  hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config glib-2.0 --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
- 
- 
- test_wrapper : test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o hspscan_corba_wrapper.o corba_singleton.o 
--	cc -g -o test_wrapper test_wrapper.o  hspscan_corba-common.o hspscan_corba-stubs.o   corba_singleton.o hspscan_corba_wrapper.o ../dynlibsrc/hsp.o ../dynlibsrc/libdyna.a ../base/libwisebase.a  `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
-+	$(CC) $(CFLAGS) $(LDFLAGS) -o test_wrapper test_wrapper.o  hspscan_corba-common.o hspscan_corba-stubs.o   corba_singleton.o hspscan_corba_wrapper.o ../dynlibsrc/hsp.o ../dynlibsrc/libdyna.a ../base/libwisebase.a  `pkg-config glib-2.0 --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
- 
- .c.o :
- 	$(CC) $(CFLAGS) $(INCFLAGS) $?
-diff --git a/src/dnaindex/assembly/makefile b/src/dnaindex/assembly/makefile
-index ef3334a..3a0bc2a 100644
---- a/src/dnaindex/assembly/makefile
-+++ b/src/dnaindex/assembly/makefile
-@@ -26,10 +26,10 @@ arraymatcher : arraymatcher.o assemblygraph.o assemblystats.o basegraph.o
- 
- 
- CC = cc
--CFLAGS = -Wall -pthread -c  -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `glib-config --cflags`
-+CFLAGS = -Wall -pthread -c  -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `pkg-config glib-2.0 --cflags`
- 
- 
--LFLAGS =  -g -L../../base/ -L../../dynlibsrc/ -lpthread `glib-config --libs` -lm
-+LFLAGS =  -g -L../../base/ -L../../dynlibsrc/ -lpthread `pkg-config glib-2.0 --libs` -lm
- 
- 
- .c.o :
-diff --git a/src/dnaindex/makefile b/src/dnaindex/makefile
-index 285e6a0..8c6a0dc 100644
---- a/src/dnaindex/makefile
-+++ b/src/dnaindex/makefile
-@@ -27,14 +27,14 @@ all: $(ASSEMBLY_OBJ)
- 
- 
- kwise : kwise.o $(ASSEMBLY_OBJ)
--	$(CC) -o kwise kwise.o $(ASSEMBLY_OBJ)  -ldyna -lwisebase $(LFLAGS) `glib-config --libs`
-+	$(CC) -o kwise kwise.o $(ASSEMBLY_OBJ)  -ldyna -lwisebase $(LFLAGS) `pkg-config glib-2.0 --libs`
- 
- arraymatcher : arraymatcher.o $(ASSEMBLY_OBJ) 
--	$(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ)  -ldyna -lwisebase $(LFLAGS) `glib-config --libs`
-+	$(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ)  -ldyna -lwisebase $(LFLAGS) `pkg-config glib-2.0 --libs`
- 
- 
- findbad_kmer : findbad_kmer.o $(ASSEMBLY_OBJ)
--	$(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ)  -ldyna -lwisebase $(LFLAGS) `glib-config --libs`
-+	$(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ)  -ldyna -lwisebase $(LFLAGS) `pkg-config glib-2.0 --libs`
- 
- make_shotgun : make_shotgun.o shotgun.o
- 	$(CC) -o make_shotgun make_shotgun.o shotgun.o -ldyna -lwisebase $(LFLAGS)
-@@ -70,10 +70,10 @@ show_euler : show_euler.o eulerindex.o singleseqspace.o
- 	$(CC) -o show_euler show_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LFLAGS)
- 
- CC = cc
--CFLAGS = -pthread -c  -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `glib-config --cflags`
-+CFLAGS = -pthread -c  -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config glib-2.0 --cflags`
- 
- 
--LFLAGS =  -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lm
-+LFLAGS =  -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config glib-2.0 --libs` -lm
- 
- 
- .c.o :
-diff --git a/src/dynlibsrc/makefile b/src/dynlibsrc/makefile
-index d1d77af..cad8900 100644
---- a/src/dynlibsrc/makefile
-+++ b/src/dynlibsrc/makefile
-@@ -78,11 +78,11 @@ DYNHELPEROBJ = packaln.o \
- 
- 
- 
--CC = cc
-+CC ?= gcc
- INCFLAGS = -I../base/
- #CFLAGS = -Wall -g -pedantic -c  -DUNIX -I../base/
--CFLAGS =  -Wall -g3 -DPTHREAD -O2 -c  -DUNIX -I../base/ `glib-config --cflags`
--#CFLAGS =   -O2 -c -pthread  -DUNIX  -I../base/ `glib-config --cflags`
-+CFLAGS +=  -DPTHREAD -c  -DUNIX -I../base/ `pkg-config glib-2.0 --cflags`
-+#CFLAGS =   -O2 -c -pthread  -DUNIX  -I../base/ `pkg-config glib-2.0 --cflags`
- #CFLAGS =   -O -c -DUNIX -DNOERROR -I../base/
- LFLAGS =  -g -L../base/ -lm 
- AR_OPTIONS = ru
-@@ -144,13 +144,13 @@ test_shadowindex : test_shadowindex.o shadowseqindex.o shadowseq.o libdyna.a
- 	$(CC) -g -o test_shadowindex test_shadowindex.o shadowseqindex.o shadowseq.o ./libdyna.a ../base/libwisebase.a -lm
- 
- test_seqhash : test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a
--	$(CC) -g -o test_seqhash `glib-config --libs` test_seqhash.o subseqhash.o hsp.o  hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a ../base/libwisebase.a -lm  
-+	$(CC) -g -o test_seqhash `pkg-config glib-2.0 --libs` test_seqhash.o subseqhash.o hsp.o  hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a ../base/libwisebase.a -lm  
- 
- test_hsp : test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o 
--	$(CC) -g -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o  ../base/libwisebase.a -lm `glib-config --libs`
-+	$(CC) -g -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o  ../base/libwisebase.a -lm `pkg-config glib-2.0 --libs`
- 
- test_topscore : test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o 
--	$(CC) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o  ../base/libwisebase.a -lm `glib-config --libs`
-+	$(CC) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o  ../base/libwisebase.a -lm `pkg-config glib-2.0 --libs`
- 
- 
- testgendb : probability.o genomicdb.o genomic.o testgendb.o sequence.o codon.o sequencedb.o complexsequence.o complexevalset.o
-diff --git a/src/external/mott/makefile b/src/external/mott/makefile
-index 8d7c1d4..940c438 100644
---- a/src/external/mott/makefile
-+++ b/src/external/mott/makefile
-@@ -14,10 +14,10 @@ libmott.a : mott_api.o gaplib.o wise2_mott_bridge.o
- wise2_mott_bridge.o : wise2_mott_bridge.c
- 	$(CC) $(CFLAGS) -I../../dynlibsrc -I../../base wise2_mott_bridge.c
- 
--CC = cc
-+CC ?= gcc
- 
--CFLAGS =  -Wall -g3 -DPTHREAD -O2 -c 
--LFLAGS =  -g -L../base/ -lm 
-+CFLAGS += -DPTHREAD -c 
-+LFLAGS = -L../base/ -lm 
- AR_OPTIONS = ru
- 
- 
-diff --git a/src/makefile b/src/makefile
-index bdff4ff..0d7c871 100644
---- a/src/makefile
-+++ b/src/makefile
-@@ -26,12 +26,12 @@
- 
- # Change the cc line to gcc if you get compiler errors
- # Most likely you have a non ANSI C compiler
--CC ?= cc
-+CC ?= gcc
- 
- # These are the CFLAGS to use. These days Wise2 is inherently
- # pthreaded, and everything is compiled with threads. More 
- # info on running threads can be found in the documentation
--CFLAGS = -c -pthread -O2 `glib-config --cflags`
-+CFLAGS += -c -pthread `pkg-config glib-2.0 --cflags`
- 
- 
- 
-diff --git a/src/models/makefile b/src/models/makefile
-index f518d0c..a297eff 100644
---- a/src/models/makefile
-+++ b/src/models/makefile
-@@ -50,6 +50,8 @@ NEWG = geneparser21.o \
- 	proteinsw.o \
- 	estquick3.o 
- 
-+EXTRALIBS += `pkg-config glib-2.0 --libs`
-+
- all : dnal psw pswdb dba estwise genewise genewisedb estwisedb genomewise sywise pseudowise promoterwise scanwisep scanwisep_wiseserver libmodel.a
- 
- libmodel.a : $(NEWG) 
-@@ -180,7 +182,7 @@ fivestarscan.o : fivestarscan.c
- 	$(CC) $(CFLAGS) fivestarscan.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I.
- 
- oldpostwise : oldpostwise.o $(NEWG) 
--	$(CC) -g -o oldpostwise oldpostwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm 
-+	$(CC) $(LDFLAGS) -o oldpostwise oldpostwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm 
- 
- testdna : testdna.o dnaalign.o seqaligndisplay.o 
- 	$(CC) -o testdna testdna.o dnaalign.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
-@@ -192,10 +194,10 @@ psw : psw.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o
- 	$(CC) -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o   $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
- 
- scanwisep.o : scanwisep.c
--	$(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `glib-config --cflags` $?
-+	$(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `pkg-config glib-2.0 --cflags` $?
- 
- hsp2aln_sw.o : hsp2aln_sw.c
--	$(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $?
-+	$(CC) $(CFLAGS) $(INCFLAGS) `pkg-config glib-2.0 --cflags` $?
- 
- scanwisep_mysql.o : scanwisep.c
- 	$(CC)  $(CFLAGS) -DSCAN_MYSQL -I../corba -I../external/mott -I../mysql/protein_index/ -I/usr/local/mysql/include scanwisep.c 
-@@ -212,10 +214,10 @@ scanwisep_corba : scanwisep_corba.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.
- 
- 
- scanwisep_wiseserver.o : scanwisep.c
--	$(CC)  $(CFLAGS) $(INCFLAGS)  -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c 
-+	$(CC)  $(LDFLAGS) $(CFLAGS) $(INCFLAGS)  -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c `pkg-config glib-2.0 --libs`
- 
- scanwisep_wiseserver : scanwisep_wiseserver.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o
--	$(CC) -o scanwisep_wiseserver scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o   ../network/net_hspscan.o $(LFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase -lm $(EXTRALIBS) -lpthread 
-+	$(CC) -o scanwisep_wiseserver scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o   ../network/net_hspscan.o $(LFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase -lm $(EXTRALIBS) -lpthread `pkg-config glib-2.0 --libs`
- 
- scanwisep_compress.o : scanwisep.c
- 	$(CC)  $(CFLAGS) -DSCAN_COMPRESS -I../dnaindex -I../network -I../socket -I../external/mott scanwisep.c 
-@@ -226,25 +228,25 @@ scanwisep_compress : scanwisep_compress.o seqaligndisplay.o proteinsw.o sw_wrap.
- 
- 
- scanwisep : scanwisep.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o
--	$(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o   $(LFLAGS)  -L../external/mott -lmott -ldyna_glib -ldyna  -lwisebase -lm $(EXTRALIBS) `glib-config --libs` -lpthread
-+	$(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o   $(LFLAGS)  -L../external/mott -lmott -ldyna_glib -ldyna  -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread
- 
- test_gwhsp : test_gwhsp.o genewisehsp.o
--	$(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `glib-config --libs` -lpthread
-+	$(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread
- 
- localcishit.o : localcishit.c
--	$(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $?
-+	$(CC) $(CFLAGS) $(INCFLAGS) `pkg-config glib-2.0 --cflags` $?
- 
- promoterwise.o : promoterwise.c  
--	$(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $?
-+	$(CC) $(CFLAGS) $(INCFLAGS) `pkg-config glib-2.0 --cflags` $?
- 
- promoterwise : promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o
--	$(CC) -g -o promoterwise promoterwise.o localdba.o  localcishit.o localcispara.o dbadisplay.o  motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o  pairwiseshortdna.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `glib-config --libs` -lpthread
-+	$(CC) $(LDFLAGS) -o promoterwise promoterwise.o localdba.o  localcishit.o localcispara.o dbadisplay.o  motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o  pairwiseshortdna.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread
- 
- test_deng : test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o
--	$(CC) -o test_deng test_deng.o  localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `glib-config --libs` -lpthread
-+	$(CC) -o test_deng test_deng.o  localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread
- 
- promotercluster : promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o
--	$(CC) -o promotercluster promotercluster.o  localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `glib-config --libs` -lpthread
-+	$(CC) -o promotercluster promotercluster.o  localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread
- 
- dnawise : dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o 
- 	$(CC) -o dnawise dnawise.o dnahmm.o dnahmmdp.o  seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm -lpthread
-@@ -275,66 +277,66 @@ makerandomdb : makerandomdb.o
- 	$(CC) -o makerandomdb makerandomdb.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
- 
- genewise : genewise.o $(NEWG) 
--	$(CC) -g -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
-+	$(CC) $(LDFLAGS) -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs`
- 
- cdnawise : cdnawise.o $(NEWG) cdnawise10.o 
--	$(CC) -g -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
-+	$(CC) $(LDFLAGS) -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
- 
- fivestar : fivestar.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o
--	$(CC) -g -o fivestar fivestar.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o  threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
-+	$(CC) $(LDFLAGS) -o fivestar fivestar.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o  threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
- 
- 
- fivestarsearch : fivestarsearch.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o
--	$(CC) -g -o fivestarsearch fivestarsearch.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o  threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
-+	$(CC) $(LDFLAGS) -o fivestarsearch fivestarsearch.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o  threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
- 
- fivestarscan : fivestarscan.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o
--	$(CC) -g -o fivestarscan fivestarscan.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o  threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
-+	$(CC) $(LDFLAGS) -o fivestarscan fivestarscan.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o  threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
- 
- 
- editdist : editdist.o editdistdp.o standardout.o seqaligndisplay.o 
--	$(CC) -g -o editdist editdist.o editdistdp.o standardout.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm
-+	$(CC) $(LDFLAGS) -o editdist editdist.o editdistdp.o standardout.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm
- 
- 
- efgw   : genewise.o $(NEWG) 
--	$(CC) -g -o genewise genewise.o  $(NEWG)  $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -lefence
-+	$(CC) $(LDFLAGS) -o genewise genewise.o  $(NEWG)  $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -lefence
- 
- 
- genewisedb : genewisedb.o $(NEWG) 
--	$(CC) -g -o genewisedb genewisedb.o  $(NEWG)  $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) 
-+	$(CC) $(LDFLAGS) -o genewisedb genewisedb.o  $(NEWG)  $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs`
- 
- estwisedb : estwisedb.o $(NEWG) 
--	$(CC) -g -o estwisedb estwisedb.o $(NEWG)  $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
-+	$(CC) $(LDFLAGS) -o estwisedb estwisedb.o $(NEWG)  $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs`
- 
- edb : estwisedb.o $(NEWG) 
--	$(CC) -g -o estwisedb estwisedb.o $(NEWG)  $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -lefence
-+	$(CC) $(LDFLAGS) -o estwisedb estwisedb.o $(NEWG)  $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -lefence
- 
- estwise : estwise.o $(NEWG) 
--	$(CC) -g -o estwise estwise.o  $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
-+	$(CC) $(LDFLAGS) -o estwise estwise.o  $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs`
- 
- 
- amplimer_resolver : amplimer_resolver.o dnaalign.o dnamatcher.o 
--	$(CC) -g -o amplimer_resolver amplimer_resolver.o dnamatcher.o dnaalign.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
-+	$(CC) $(LDFLAGS) -o amplimer_resolver amplimer_resolver.o dnamatcher.o dnaalign.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
- 
- genomewise : genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneutil.o geneoutput.o
--	$(CC) -g -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
-+	$(CC) $(LDFLAGS) -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
- 
- sywise : sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o geneutil.o standardout.o
--	$(CC) -g -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o  standardout.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
-+	$(CC) $(LDFLAGS) -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o  standardout.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
- 
- alignwise : alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o
--	$(CC) -g -o alignwise alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
-+	$(CC) $(LDFLAGS) -o alignwise alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
- 
- test_splice : test_splice.o  aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o
--	$(CC) -g -o test_splice test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
-+	$(CC) $(LDFLAGS) -o test_splice test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
- 
- statwise : statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o
--	$(CC) -g -o statwise statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
-+	$(CC) $(LDFLAGS) -o statwise statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
- 
- pseudowise : pseudowise.o pseudowise7.o $(NEWG) 
--	$(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
-+	$(CC) $(LDFLAGS) -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs`
- 
- clonewise : clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o
--	$(CC) -g -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
-+	$(CC) $(LDFLAGS) -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
- 
- 
- HMMER_LIBS = ../HMMer2/
-@@ -345,11 +347,11 @@ HMMER_DEFINE =
- CC = cc
- #CFLAGS = -c -O2  -pg -I../base/ -I../dynlibsrc/
- #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE  -DUNIX  -I../base/ -I../dynlibsrc/ -I.
--CFLAGS = -c -g3 -O2  -DUNIX  -I../base/ -I../dynlibsrc/ -I. -pthread `glib-config --cflags`
--#CFLAGS = -c  -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `glib-config --cflags`
-+CFLAGS = -c -g3 -O2  -DUNIX  -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config glib-2.0 --cflags`
-+#CFLAGS = -c  -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config glib-2.0 --cflags`
- #LFLAGS =  -L../base/ -L../dynlibsrc/ -L../HMMer2/  
- 
--LFLAGS =  -g -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `glib-config --libs`
-+LFLAGS =  -g -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `pkg-config glib-2.0 --libs`
- AR_OPTIONS = ru
- 
- RANLIB_NEEDED = 0
-diff --git a/src/network/makefile b/src/network/makefile
-index 303c2da..e607310 100644
---- a/src/network/makefile
-+++ b/src/network/makefile
-@@ -3,8 +3,8 @@
- 
- CC = cc
- INCFLAGS = -I../base/  -I../socket -I../dynlibsrc -I../dnaindex
--CFLAGS =   -O2 -g3 -c -pthread  -DUNIX  -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `glib-config --cflags`
--LFLAGS =  -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `glib-config --libs`
-+CFLAGS =   -O2 -g3 -c -pthread  -DUNIX  -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `pkg-config glib-2.0 --cflags`
-+LFLAGS =  -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `pkg-config glib-2.0 --libs`
- AR_OPTIONS = ru
- 
- RANLIB_NEEDED = 0
-diff --git a/src/snp/makefile b/src/snp/makefile
-index ccf750a..2b83c43 100644
---- a/src/snp/makefile
-+++ b/src/snp/makefile
-@@ -2,12 +2,12 @@
- .SUFFIXES :  .dy
- 
- 
--CC = cc
-+CC ?= gcc
- #CFLAGS = -c -O2  -pg -I../base/ -I../dynlibsrc/
- #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE  -DUNIX  -I../base/ -I../dynlibsrc/ -I.
--CFLAGS = -c -g3 -O2  -DUNIX  -I../base/ -I../dynlibsrc/ -I. -pthread `glib-config --cflags`
-+CFLAGS += -c -DUNIX  -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config glib-2.0  --cflags`
- 
--LFLAGS =  -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lpthread -lm
-+LFLAGS =  -L../base/ -L../dynlibsrc/ -lpthread `pkg-config glib-2.0 --libs` -lpthread -lm
- AR_OPTIONS = ru
- 
- RANLIB_NEEDED = 0
-@@ -16,7 +16,7 @@ RANLIB_NEEDED = 0
- 	$(CC) $(CFLAGS) $(INCFLAGS) $?
- 
- test_est : test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o 
--	$(CC) -o test_est test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o ../dynlibsrc/libdyna.a ../base/libwisebase.a $(LFLAGS)
-+	$(CC) $(LDFLAGS) -o test_est test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o ../dynlibsrc/libdyna.a ../base/libwisebase.a $(LFLAGS)
- 
- INCFLAGS = -I../base/ -I../dynlibsrc/
- DFLAGS = -l -D -n Wise2_ -a _api.h -b _api.t -pthreads -dbtrace 5 -nocwarn
diff --git a/sci-biology/wise/files/wise-2.4.0_alpha-glibc-2.10.patch b/sci-biology/wise/files/wise-2.4.0_alpha-glibc-2.10.patch
deleted file mode 100644
index 42af0c7e849b..000000000000
--- a/sci-biology/wise/files/wise-2.4.0_alpha-glibc-2.10.patch
+++ /dev/null
@@ -1,302 +0,0 @@
-diff --git a/src/HMMer2/sqio.c b/src/HMMer2/sqio.c
-index 5889e7d..bc95629 100644
---- a/src/HMMer2/sqio.c
-+++ b/src/HMMer2/sqio.c
-@@ -213,7 +213,7 @@ readline(FILE *f, char *s)
-     }
- }
- 
--/* Function: getline()
-+/* Function: get_line()
-  * Date:     SRE, Tue Mar  3 08:30:01 1998 [St. Louis]
-  *
-  * Purpose:  read a line from a sequence file into V->sbuffer.
-@@ -229,7 +229,7 @@ readline(FILE *f, char *s)
-  * Returns:  (void)
-  */
- static void 
--getline(struct ReadSeqVars *V)
-+get_line(struct ReadSeqVars *V)
- {
-   char *cp;
-   
-@@ -299,7 +299,7 @@ readLoop(int addfirst, int (*endTest)(char *,int *), struct ReadSeqVars *V)
-   V->seqlen = 0;
-   if (addfirst) addseq(V->sbuffer, V);
-   do {
--    getline(V);
-+    get_line(V);
- 	/* feof() alone is a bug; files not necessarily \n terminated */
-     if (*(V->sbuffer) == '\0' && feof(V->f))
-       done = TRUE;
-@@ -327,7 +327,7 @@ readPIR(struct ReadSeqVars *V)
-   char *sptr;
- 				/* load first line of entry  */
-   while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
--    getline(V);
-+    get_line(V);
-   if (feof(V->f)) return;
- 
-   if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL)
-@@ -336,7 +336,7 @@ readPIR(struct ReadSeqVars *V)
-       SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID);
-     }
-   do {
--    getline(V);
-+    get_line(V);
-     if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0)
-       SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC);
-     else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0)
-@@ -345,7 +345,7 @@ readPIR(struct ReadSeqVars *V)
- 	  SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC);
-       }
-   } while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0));
--  getline(V);			/* skip next line, coords */
-+  get_line(V);			/* skip next line, coords */
- 
-   readLoop(0, endPIR, V);
- 
-@@ -359,7 +359,7 @@ readPIR(struct ReadSeqVars *V)
-   /* get next line
-    */
-   while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
--    getline(V);
-+    get_line(V);
- }
- 
- 
-@@ -377,7 +377,7 @@ readIG(struct ReadSeqVars *V)
-   char *nm;
- 				/* position past ';' comments */
-   do {
--    getline(V);
-+    get_line(V);
-   } while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) ));
- 
-   if (!feof(V->f))
-@@ -389,7 +389,7 @@ readIG(struct ReadSeqVars *V)
-     }
-   
-   while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';'))))
--    getline(V);
-+    get_line(V);
- }
- 
- static int 
-@@ -411,7 +411,7 @@ readStrider(struct ReadSeqVars *V)
- 	  if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL)
- 	    SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME);
- 	}
--      getline(V);
-+      get_line(V);
-     }
- 
-   if (! feof(V->f))
-@@ -420,7 +420,7 @@ readStrider(struct ReadSeqVars *V)
-   /* load next line
-    */
-   while ((!feof(V->f)) && (*V->sbuffer != ';')) 
--    getline(V);
-+    get_line(V);
- }
- 
- 
-@@ -438,7 +438,7 @@ readGenBank(struct ReadSeqVars *V)
-   int   in_definition;
- 
-   while (strncmp(V->sbuffer, "LOCUS", 5) != 0)
--    getline(V);
-+    get_line(V);
- 
-   if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL)
-     {
-@@ -449,7 +449,7 @@ readGenBank(struct ReadSeqVars *V)
-   in_definition = FALSE;
-   while (! feof(V->f))
-     {
--      getline(V);
-+      get_line(V);
-       if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer)
- 	{
- 	  if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL)
-@@ -482,11 +482,11 @@ readGenBank(struct ReadSeqVars *V)
- 
- 
-   while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer))))
--    getline(V);
-+    get_line(V);
- 				/* SRE: V->s now holds "//", so sequential
- 				   reads are wedged: fixed Tue Jul 13 1993 */
-   while (!feof(V->f) && strstr(V->sbuffer, "LOCUS  ") != V->sbuffer)
--    getline(V);
-+    get_line(V);
- }
- 
- static int
-@@ -515,7 +515,7 @@ readGCGdata(struct ReadSeqVars *V)
-     Die("bogus GCGdata format? %s", V->sbuffer);
- 
- 				/* second line contains free text description */
--  getline(V);
-+  get_line(V);
-   SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC);
- 
-   if (binary) {
-@@ -535,7 +535,7 @@ readGCGdata(struct ReadSeqVars *V)
-   else readLoop(0, endGCGdata, V);
-   
-   while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
--    getline(V);
-+    get_line(V);
- }
- 
- static int
-@@ -555,12 +555,12 @@ readPearson(struct ReadSeqVars *V)
-   if ((sptr = strtok(NULL, "\n")) != NULL)
-     SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC);
- 				/* workaround for long NCBI NR lines */
--  while (V->longline && ! feof(V->f)) getline(V);
-+  while (V->longline && ! feof(V->f)) get_line(V);
- 
-   readLoop(0, endPearson, V);
- 
-   while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
--    getline(V);
-+    get_line(V);
- }
- 
- 
-@@ -587,7 +587,7 @@ readEMBL(struct ReadSeqVars *V)
- 
- 				/* make sure we have first line */
-   while (!feof(V->f) && strncmp(V->sbuffer, "ID  ", 4) != 0)
--    getline(V);
-+    get_line(V);
- 
-   if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL)
-     {
-@@ -596,7 +596,7 @@ readEMBL(struct ReadSeqVars *V)
-     }
- 
-   do {
--    getline(V);
-+    get_line(V);
-     if (!feof(V->f) && strstr(V->sbuffer, "AC  ") == V->sbuffer)
-       {
- 	if ((sptr = strtok(V->sbuffer+5, ";  \t\n")) != NULL)
-@@ -620,7 +620,7 @@ readEMBL(struct ReadSeqVars *V)
- 
- 				/* load next record's ID line */
-   while (!feof(V->f) && strncmp(V->sbuffer, "ID  ", 4) != 0)
--    getline(V);
-+    get_line(V);
- }
- 
- 
-@@ -636,7 +636,7 @@ readZuker(struct ReadSeqVars *V)
- {
-   char *sptr;
- 
--  getline(V);  /*s == "seqLen seqid string..."*/
-+  get_line(V);  /*s == "seqLen seqid string..."*/
- 
-   if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL)
-     SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
-@@ -647,7 +647,7 @@ readZuker(struct ReadSeqVars *V)
-   readLoop(0, endZuker, V);
- 
-   while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '('))))
--    getline(V);
-+    get_line(V);
- }
- 
- static void 
-@@ -669,7 +669,7 @@ readUWGCG(struct ReadSeqVars *V)
- 
-   do {
-     done = feof(V->f);
--    getline(V);
-+    get_line(V);
-     if (! done) addseq(V->sbuffer, V);
-   } while (!done);
- }
-@@ -681,7 +681,7 @@ readSquid(struct ReadSeqVars *V)
-   char *sptr;
-   int   dostruc = FALSE;
- 
--  while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V);
-+  while (strncmp(V->sbuffer, "NAM ", 4) != 0) get_line(V);
- 
-   if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL)
-     SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
-@@ -689,7 +689,7 @@ readSquid(struct ReadSeqVars *V)
-   /*CONSTCOND*/
-   while (1)
-     {
--      getline(V);
-+      get_line(V);
-       if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; }
- 
-       if (strncmp(V->sbuffer, "SRC ", 4) == 0)
-@@ -721,14 +721,14 @@ readSquid(struct ReadSeqVars *V)
-   while (1)
-     {
- 				/* sequence line */
--      getline(V);
-+      get_line(V);
-       if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0) 
- 	break;
-       addseq(V->sbuffer, V);
- 				/* structure line */
-       if (dostruc)
- 	{
--	  getline(V);
-+	  get_line(V);
- 	  if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; }
- 	  addstruc(V->sbuffer, V);
- 	}
-@@ -736,7 +736,7 @@ readSquid(struct ReadSeqVars *V)
- 
- 
-   while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0)
--    getline(V);
-+    get_line(V);
- }
- 
- 
-@@ -816,7 +816,7 @@ SeqfileOpen(char *filename, int format, char *env)
- 
-   /* Load the first line.
-    */
--  getline(dbfp);
-+  get_line(dbfp);
- 
-   return dbfp;
- }
-@@ -833,7 +833,7 @@ SeqfilePosition(SQFILE *sqfp, long offset)
-     Die("SeqfilePosition() failed: in a nonrewindable data file or stream");
- 
-   fseek(sqfp->f, offset, SEEK_SET);
--  getline(sqfp);
-+  get_line(sqfp);
- }
- 
- 
-@@ -853,7 +853,7 @@ SeqfileRewind(SQFILE *sqfp)
-   if (sqfp->ali_aseqs != NULL) sqfp->ali_curridx = 0;
-   else {
-     rewind(sqfp->f);
--    getline(sqfp);
-+    get_line(sqfp);
-   }
- }
- 
-@@ -949,7 +949,7 @@ ReadSeq(SQFILE *V, int format, char **ret_seq, SQINFO *sqinfo)
-       do {			/* skip leading comments on GCG file */
- 	gotuw = (strstr(V->sbuffer,"..") != NULL);
- 	if (gotuw) readUWGCG(V);
--	getline(V);
-+	get_line(V);
-       } while (! feof(V->f));
-       break;
- 
diff --git a/sci-biology/wise/files/wise-api.tex.patch b/sci-biology/wise/files/wise-api.tex.patch
deleted file mode 100644
index 827ce4cdfa7a..000000000000
--- a/sci-biology/wise/files/wise-api.tex.patch
+++ /dev/null
@@ -1,38 +0,0 @@
---- api.tex.old	2005-03-06 11:31:59.862760952 -0500
-+++ api.tex	2005-03-06 11:42:31.375756384 -0500
-@@ -204,7 +204,7 @@
- \item Build two Sequence objects, from a file or strings (\ref{object_Sequence})
- \item Optionally convert the Sequence objects into Protein objects (\ref{object_Protein}). This ensures you have proteins
- \item Read in the comparison matrix using CompMat (\ref{object_CompMat})
--\item Use one of the algorithm calls in sw_wrap module (\ref{module_sw_wrap})
-+\item Use one of the algorithm calls in sw\_wrap module (\ref{module_sw_wrap})
- \item Show the alignment using a call in the seqaligndisaply module (\ref{module_seqaligndisplay})
- \end{itemize}
- 
-@@ -213,7 +213,7 @@
- \item Read in a sequence object and convert it to a protein object (\ref{object_Protein},\ref{object_Sequence})
- \item Make a protein database from the single protein object (\ref{object_ProteinDB})
- \item Make a protein database from a single fasta file (\ref{object_ProteinDB})
--\item Using one of the calls to the sw_wrap module, make a Hscore object (\ref{module_sw_wrap})
-+\item Using one of the calls to the sw\_wrap module, make a Hscore object (\ref{module_sw_wrap})
- \item Show the Hscore object using a show function (\ref{object_Hscore})
- \item Retrieve individual protein objects from the database by taking out the
- DataEntry objects (\ref{object_DataEntry}) and passing them into the ProteinDB object (\ref{object_ProteinDB}), giving you a protein object
-@@ -232,7 +232,7 @@
- \item Read in a codon table (\ref{object_CodonTable})
- \item Make a random DNA model (\ref{object_RandomModelDNA})
- \item Make an algorithm type (\ref{module_gwrap})
--\item Build an entire parameter set for genewise using Wise2::GeneParameter21_wrap (\ref{module_gwrap})
-+\item Build an entire parameter set for genewise using Wise2::GeneParameter21\_wrap (\ref{module_gwrap})
- \item Run the actual algorithm (\ref{module_gwrap})
- \item show the alignment using genedisplay (\ref{module_gwrap})
- \end{itemize}
-@@ -5055,7 +5055,7 @@
- Member functions of RandomModel
- 
- \section{sequence\_codon}
--\label{module_sequence\_codon}
-+\label{module_sequence_codon}
- This module only contains factory methods
- 
- \subsection{sequence\_codon factory methods}
diff --git a/sci-biology/wise/files/wise-env b/sci-biology/wise/files/wise-env
deleted file mode 100644
index 3f781c80833b..000000000000
--- a/sci-biology/wise/files/wise-env
+++ /dev/null
@@ -1 +0,0 @@
-WISECONFIGDIR="/usr/share/wise/wisecfg"
diff --git a/sci-biology/wise/wise-2.4.0_alpha.ebuild b/sci-biology/wise/wise-2.4.0_alpha.ebuild
index 3d4f0955d848..aa971e0c6932 100644
--- a/sci-biology/wise/wise-2.4.0_alpha.ebuild
+++ b/sci-biology/wise/wise-2.4.0_alpha.ebuild
@@ -7,7 +7,8 @@ inherit eutils toolchain-funcs versionator
 
 DESCRIPTION="Intelligent algorithms for DNA searches"
 HOMEPAGE="http://www.ebi.ac.uk/Wise2/"
-SRC_URI="ftp://ftp.ebi.ac.uk/pub/software/${PN}2/${PN}$(delete_version_separator 3).tar.gz"
+SRC_URI="ftp://ftp.ebi.ac.uk/pub/software/${PN}2/${PN}$(delete_version_separator 3).tar.gz
+	https://dev.gentoo.org/~mgorny/dist/${P}-patchset.tar.bz2"
 
 LICENSE="BSD"
 SLOT="0"
@@ -25,12 +26,12 @@ S="${WORKDIR}"/${PN}$(delete_version_separator 3)
 
 src_prepare() {
 	epatch \
-		"${FILESDIR}"/${P}-glibc-2.10.patch \
-		"${FILESDIR}"/${P}-cflags.patch
+		"${WORKDIR}"/${P}-patchset/${P}-glibc-2.10.patch \
+		"${WORKDIR}"/${P}-patchset/${P}-cflags.patch
 	cd "${S}"/docs || die
 	cat "${S}"/src/models/*.tex "${S}"/src/dynlibsrc/*.tex | perl gettex.pl > temp.tex || die
 	cat wise2api.tex temp.tex apiend.tex > api.tex || die
-	epatch "${FILESDIR}"/${PN}-api.tex.patch
+	epatch "${WORKDIR}"/${P}-patchset/${PN}-api.tex.patch
 }
 
 src_compile() {
@@ -68,5 +69,5 @@ src_install() {
 		insinto /usr/share/doc/${PF}
 		doins "${S}"/docs/*.ps
 	fi
-	newenvd "${FILESDIR}"/${PN}-env 24wise || die "Failed to install env file"
+	newenvd "${WORKDIR}"/${P}-patchset/${PN}-env 24wise || die "Failed to install env file"
 }