sci-biology/allpathslg: [QA] Move patches to a distfile

Closes: https://bugs.gentoo.org/620610

4 files changed, 7 insertions, 1808 deletions

diff --git a/sci-biology/allpathslg/Manifest b/sci-biology/allpathslg/Manifest
index c87071a88937..22364d00b079 100644
--- a/sci-biology/allpathslg/Manifest
+++ b/sci-biology/allpathslg/Manifest
@@ -1 +1,2 @@
-DIST allpathslg-52488.tar.gz 3121949 SHA256 035b49cb21b871a6b111976757d7aee9c2513dd51af04678f33375e620998542 SHA512 c44ef1a3ed5b343bf096663309cc399e79d65e83175232743cf330fd0d426633bd0d388922fd0c73ac0927d85ea9005549c8e4f7711c79fea7107068510ef30d WHIRLPOOL c63a13450c55fce8f2c5399bdd5d8f32939e31d9d13a120835b1d826ae96e251fea81caa134d5d45ad857af0777c22e4ad1d894c81a74db6d83a7d9ad83b12b4
+DIST allpathslg-52488-patchset.tar.bz2 11405 BLAKE2B 7a4c36884ac95a4eb23291720e422ce1ec41d0bea3a0b10582aa1d8154234971eb8d06979a969e65c1ec1eab031d2500a1ec40809019c8b4aa1d1d2e81427dbe SHA512 a1d58c131afeef04a9d7a2520fcd28a853317323fdcab1a253cb2548546bbc559993c74a68a8032a5d0e865ac2c2d53ff6b4c149aade2d1f87a2ab4116ebe4cc
+DIST allpathslg-52488.tar.gz 3121949 BLAKE2B b75904f9e8256a14c97abae45a0cb41718f95d27a4a072b6144bd125abb57682faa180de6a18399ab4fa43988344c436ca1eab8412433353fcc746c432c33031 SHA512 c44ef1a3ed5b343bf096663309cc399e79d65e83175232743cf330fd0d426633bd0d388922fd0c73ac0927d85ea9005549c8e4f7711c79fea7107068510ef30d
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;
- 
- /////////////////////////////////////////////////////////////////////////////
- //