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 +23,11 @@
 #include "paths/long/ReadOriginTracker.h"
 #include "paths/long/EvalByReads.h"
 
+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;
--- 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;
 
 /////////////////////////////////////////////////////////////////////////////
 //