diff options
| author |   Michał Górny <mgorny@gentoo.org> | 2017-12-10 00:12:24 +0100 |
|---|---|---|
| committer | Michał Górny <mgorny@gentoo.org> | 2017-12-10 00:13:08 +0100 |
| commit | b2afaced4f1f7c81e59293698518d9b4f6f8b414 (patch) | |
| tree | 6c2ed2d658c703cebb0c50acf7d9585bcc04242b /sci-biology/allpathslg | |
| parent | dev-vcs/*: Update Manifest hashes (diff) | |
| download | gentoo-b2afaced4f1f7c81e59293698518d9b4f6f8b414.tar.gz gentoo-b2afaced4f1f7c81e59293698518d9b4f6f8b414.tar.bz2 gentoo-b2afaced4f1f7c81e59293698518d9b4f6f8b414.zip | |
sci-biology/allpathslg: [QA] Move patches to a distfile
Closes: https://bugs.gentoo.org/620610
Diffstat (limited to 'sci-biology/allpathslg')
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; - - ///////////////////////////////////////////////////////////////////////////// - // |