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1771 lines
48 KiB
1771 lines
48 KiB
Remove 'using namespace std' causing massive havoc with newly
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introduced std::align in GCC-5. Fix bug
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https://bugs.gentoo.org/show_bug.cgi?id=568440
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--- allpathslg-52488/src/agp/AgpFile.cc
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+++ allpathslg-52488/src/agp/AgpFile.cc
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@@ -4,6 +4,8 @@
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#include "agp/AgpFile.h"
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#include "TokenizeString.h"
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+using std::cerr;
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+
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char agp_contig::TypeChar_() const
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{
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switch ( type_ )
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--- allpathslg-52488/src/agp/AgpFile.h
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+++ allpathslg-52488/src/agp/AgpFile.h
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@@ -9,6 +9,8 @@
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#include "agp/AgpMods.h"
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+using std::max;
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+
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class agp_entry
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{
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public:
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--- allpathslg-52488/src/agp/AgpMods.cc
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+++ allpathslg-52488/src/agp/AgpMods.cc
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@@ -7,6 +7,8 @@
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#include "system/System.h"
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+using std::istrstream;
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+
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bool
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agp_mods::SuperShouldBeRemoved( int super_id ) const
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{
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--- allpathslg-52488/src/agp/AgpMods.h
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+++ allpathslg-52488/src/agp/AgpMods.h
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@@ -7,6 +7,8 @@
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#include "String.h"
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#include "Vec.h"
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+using std::swap;
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+
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// The class contig_range provides begin and end positions on a
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// contig. If the end position is before the begin position, the
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// range is considered reversed. If a length is provided, the range
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--- allpathslg-52488/src/allpaths_cache/CacheReadsMerge.cc
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+++ allpathslg-52488/src/allpaths_cache/CacheReadsMerge.cc
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@@ -56,6 +56,8 @@
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#include "feudal/VirtualMasterVec.h"
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#include "random/Shuffle.h"
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+using std::map;
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+
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typedef VirtualMasterVec<BaseVec> VBaseVecVec;
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typedef VirtualMasterVec<QualVec> VQualVecVec;
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--- allpathslg-52488/src/AnAssemblyClass.h
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+++ allpathslg-52488/src/AnAssemblyClass.h
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@@ -19,6 +19,8 @@
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#include "ReadLocation.h"
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#include "ReadPairing.h"
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+using std::map;
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+
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class assembly;
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class super {
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--- allpathslg-52488/src/efasta/EfastaTools.cc
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+++ allpathslg-52488/src/efasta/EfastaTools.cc
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@@ -19,6 +19,8 @@
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#include "math/Array.h"
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#include <iostream>
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+using std::set;
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+
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#define Err(message) \
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{ cout << message << endl << "\nInvalid.\n" << endl; \
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TracebackThisProcess( ); }
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--- allpathslg-52488/src/Equiv.cc
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+++ allpathslg-52488/src/Equiv.cc
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@@ -9,6 +9,8 @@
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#include "Equiv.h"
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#include "Vec.h"
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+using std::swap;
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+
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bool equivalence_relation::equiv(int a, int b) const
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{ if ( a == b ) return true;
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int c = a;
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--- allpathslg-52488/src/FastaFilestream.cc
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+++ allpathslg-52488/src/FastaFilestream.cc
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@@ -13,6 +13,8 @@
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#include <strstream>
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+using std::string;
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+
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template <typename vecT, typename seqT, typename convT, typename verifT>
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FastaFilestream<vecT,seqT,convT,verifT>::FastaFilestream( const String& filename,
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FastaNameParser* name_parser )
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--- allpathslg-52488/src/FastaFilestreamPreview.cc
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+++ allpathslg-52488/src/FastaFilestreamPreview.cc
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@@ -11,6 +11,8 @@
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#include <algorithm>
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+using std::streamoff;
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+
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FastaFilestreamPreview::FastaFilestreamPreview(istream& filestream)
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: max_sequence_size_(0), start_offset_(0)
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{
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--- allpathslg-52488/src/FastaFilestreamPreview.h
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+++ allpathslg-52488/src/FastaFilestreamPreview.h
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@@ -12,6 +12,8 @@
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#include "Vec.h"
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+using std::streampos;
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+
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// FastaFilestreamPreview understands just enough about the fasta
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// format to be able to count the number of sequences in the specified
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// filestream and to know where each sequence starts in that filestream.
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--- allpathslg-52488/src/Fastavector.cc
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+++ allpathslg-52488/src/Fastavector.cc
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@@ -14,6 +14,8 @@
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#include <istream>
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#include <string>
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+using std::max;
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+
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// Split this into chunks, separated by gaps ('n'), and return each chunk as a
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// gapless fastavector.
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// TODO: generalize this into a templatized STL algorithm.
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--- allpathslg-52488/src/Fastavector.h
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+++ allpathslg-52488/src/Fastavector.h
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@@ -24,6 +24,9 @@
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#include <iostream>
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#include <unistd.h>
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+using std::string;
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+using std::istringstream;
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+
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typedef std::tuple<String, int, int> FastaRegion;
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class fastaindex {
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--- allpathslg-52488/src/FetchReads.cc
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+++ allpathslg-52488/src/FetchReads.cc
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@@ -36,6 +36,8 @@
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#include "Qualvector.h"
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#include "random/Random.h"
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+using std::istringstream;
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+
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// Heuristic constants:
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namespace
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--- allpathslg-52488/src/feudal/BaseVec.cc
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+++ allpathslg-52488/src/feudal/BaseVec.cc
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@@ -21,6 +21,7 @@
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using std::ostream;
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using std::cout;
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using std::endl;
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+using std::max_element;
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// Cap: in a given basevector, replace any sequence of N > n identical
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// bases by n of the same base.
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--- allpathslg-52488/src/graph/Digraph.cc
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+++ allpathslg-52488/src/graph/Digraph.cc
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@@ -17,6 +17,9 @@
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#include "graph/Digraph.h"
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#include "math/Functions.h"
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+using std::make_pair;
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+using std::priority_queue;
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+
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void digraph::TransferEdges( int v, int w, const Bool enter_only )
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{ ForceAssert( v != w );
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--- allpathslg-52488/src/graph/Digraph.h
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+++ allpathslg-52488/src/graph/Digraph.h
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@@ -52,6 +52,8 @@
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#include "system/TraceVal.h"
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#include <cstddef>
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+using std::function;
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+
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typedef pair<int, int> VertexPair;
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typedef int vrtx_t;
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--- allpathslg-52488/src/graph/DigraphTemplate.h
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+++ allpathslg-52488/src/graph/DigraphTemplate.h
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@@ -34,6 +34,8 @@
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#include "graph/Digraph.h"
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#include <cstddef>
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+using std::make_pair;
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+
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template<class E> vec<int> digraphE<E>:: EdgesBoundedBy( const int e1, const int e2,
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const vec<int>& to_left, const vec<int>& to_right ) const
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{ int v = to_right[e1], w = to_left[e2];
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--- allpathslg-52488/src/graph/GraphAlgorithms.h
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+++ allpathslg-52488/src/graph/GraphAlgorithms.h
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@@ -9,7 +9,7 @@
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#ifndef GRAPH__GRAPH_ALGORITHMS__H_
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#define GRAPH__GRAPH_ALGORITHMS__H_
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-
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+using std::map;
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// -------------- Union Find ---------------
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//
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--- allpathslg-52488/src/IndexedAlignmentPlusVector.h
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+++ allpathslg-52488/src/IndexedAlignmentPlusVector.h
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@@ -15,6 +15,8 @@
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#include "Alignment.h"
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+using std::streampos;
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+using std::streamoff;
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// This class encapsulates the header information for both vectors and indices.
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--- allpathslg-52488/src/kmers/kmer_parcels/KmerParcelsClasses.h
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+++ allpathslg-52488/src/kmers/kmer_parcels/KmerParcelsClasses.h
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@@ -6,6 +6,9 @@
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// Institute is not responsible for its use, misuse, or functionality. //
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///////////////////////////////////////////////////////////////////////////////
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+using std::hex;
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+using std::dec;
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+
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// ---------------------------------
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// NaifTimer
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// ---------------------------------
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--- allpathslg-52488/src/kmers/naif_kmer/KernelErrorFinder.h
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+++ allpathslg-52488/src/kmers/naif_kmer/KernelErrorFinder.h
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@@ -13,8 +13,8 @@
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#include "kmers/naif_kmer/LockedBlocks.h"
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#include "kmers/naif_kmer/Kmers.h"
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-
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-
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+using std::make_pair;
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+using std::stringstream;
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--- allpathslg-52488/src/kmers/naif_kmer/Kmers.h
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+++ allpathslg-52488/src/kmers/naif_kmer/Kmers.h
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@@ -14,7 +14,7 @@
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#include "kmers/naif_kmer/KmerFunctions.h"
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-
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+using std::string;
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// ---- 256 random 64bit numbers to compute hash key
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--- allpathslg-52488/src/layout/ContigActualloc.h
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+++ allpathslg-52488/src/layout/ContigActualloc.h
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@@ -17,6 +17,8 @@
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#include "system/Crash.h"
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#include "Misc.h"
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+using std::set;
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+using std::map;
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//
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// Class contig_actualloc
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--- allpathslg-52488/src/lookup/ImperfectLookup.h
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+++ allpathslg-52488/src/lookup/ImperfectLookup.h
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@@ -51,6 +51,8 @@
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#include "lookup/LookupTools.h"
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#include "lookup/AlignCollector.h"
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+using std::auto_ptr;
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+
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class TaskTimer;
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|
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--- allpathslg-52488/src/lookup/LookAlign.cc
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+++ allpathslg-52488/src/lookup/LookAlign.cc
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@@ -29,6 +29,8 @@
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#include "random/Random.h"
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#include "system/ParsedArgs.h"
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+using std::istrstream;
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+
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String QUERY("QUERY");
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void look_align::ResetFromAlign(const align & al, const basevector & b1,
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--- allpathslg-52488/src/lookup/LookupTable.h
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+++ allpathslg-52488/src/lookup/LookupTable.h
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@@ -18,6 +18,8 @@
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#include <set>
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+using std::set;
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+
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typedef pair<unsigned int, unsigned int> LocSeq;
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///
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--- allpathslg-52488/src/lookup/QueryLookupTableCore.cc
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+++ allpathslg-52488/src/lookup/QueryLookupTableCore.cc
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@@ -465,6 +465,9 @@
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#include "system/ParsedArgs.h"
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#include "system/file/FileReader.h"
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+using std::istrstream;
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+using std::less_equal;
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+
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#define ABORT(MSG) \
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{ out << MSG << " Abort." << endl << endl; \
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exit(1); }
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--- allpathslg-52488/src/lookup/ShortQueryLookup.cc
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+++ allpathslg-52488/src/lookup/ShortQueryLookup.cc
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@@ -32,6 +32,8 @@
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#include "lookup/AlignCollector.h"
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#include "lookup/ImperfectLookup.h"
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+using std::ios_base;
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+
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// Run an alignment processing chain: seqs -> look -> receiver -> aligns
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// That is, look turns seqs into hits, which receiver accepts
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// and turns into alignments which are passed to aligns. The
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--- allpathslg-52488/src/Map.h
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+++ allpathslg-52488/src/Map.h
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@@ -23,7 +23,7 @@
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#include <unordered_map>
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#include <ext/hash_map>
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using namespace __gnu_cxx;
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-
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+using std::map;
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template <class K, class V, class C=std::less<K>>
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using StdMap = std::map<K,V,C,typename DefaultAllocator<std::pair<K const,V>>::type>;
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--- allpathslg-52488/src/math/Array.h
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+++ allpathslg-52488/src/math/Array.h
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@@ -13,6 +13,8 @@
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#include "Vec.h"
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#include "Map.h"
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+using std::fill;
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+
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// ==============================================================================
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// A fixed-size simple c-style 2D array that allocates faster than vec< vec<T> >
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// The elements are uninitialized.
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--- allpathslg-52488/src/math/Functions.cc
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+++ allpathslg-52488/src/math/Functions.cc
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@@ -10,7 +10,7 @@
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#include "STLExtensions.h"
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#include "math/Functions.h"
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-
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+using std::make_pair;
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/* CombineNormalDistribution Filipe Ribeiro 2009-06-22
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--- allpathslg-52488/src/math/Functions.h
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+++ allpathslg-52488/src/math/Functions.h
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@@ -15,6 +15,10 @@
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#include <cmath>
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#include <numeric>
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+using std::min;
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+using std::cerr;
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+using std::swap;
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+
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// ===========================================================================
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//
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// Min functions
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--- allpathslg-52488/src/math/HoInterval.cc
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+++ allpathslg-52488/src/math/HoInterval.cc
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@@ -10,6 +10,8 @@
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#include "math/HoInterval.h"
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#include "STLExtensions.h"
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+using std::make_pair;
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+
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bool ho_interval::Merge(const ho_interval & o) {
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if (!Meets(*this,o)) return false;
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*this = Span(*this, o);
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--- allpathslg-52488/src/math/HoInterval.h
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+++ allpathslg-52488/src/math/HoInterval.h
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@@ -14,6 +14,8 @@
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#include "feudal/MasterVec.h"
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#include "feudal/SerfVec.h"
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+using std::max;
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+
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/// Class: ho_interval
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/// A half-open interval [a, b).
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class ho_interval {
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--- allpathslg-52488/src/math/IntFunction.h
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+++ allpathslg-52488/src/math/IntFunction.h
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@@ -21,6 +21,8 @@
|
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|
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#include "MainTools.h"
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+using std::deque;
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+using std::fixed;
|
|
|
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#define __INT_FUNCTION_BINARY_VERSION__ 2
|
|
|
|
--- allpathslg-52488/src/PackAlign.h
|
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+++ allpathslg-52488/src/PackAlign.h
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@@ -133,6 +133,8 @@
|
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#include "pairwise_aligners/Mutmer.h"
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#include "feudal/BinaryStream.h"
|
|
|
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+using std::make_pair;
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+
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const int Bits2 = 3, Bits3 = 7, Bits4 = 15, Bits10 = 1023, Bits12 = 4095,
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Bits16 = 65535;
|
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|
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--- allpathslg-52488/src/PairsManager.h
|
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+++ allpathslg-52488/src/PairsManager.h
|
|
@@ -61,6 +61,7 @@
|
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#include "feudal/BinaryStream.h"
|
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#include <cstddef>
|
|
|
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+using std::make_pair;
|
|
|
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class PairsManager; // forward declaration
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|
|
|
--- allpathslg-52488/src/pairwise_aligners/MakeAlignsMethod.cc
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+++ allpathslg-52488/src/pairwise_aligners/MakeAlignsMethod.cc
|
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@@ -19,6 +19,9 @@
|
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#include "pairwise_aligners/AlignFromMutmers.h"
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#include "pairwise_aligners/SmithWatBandedA.h"
|
|
|
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+using std::map;
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+using std::set;
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+
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// If there's a perfect match of length at least perf but we produced no proper
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// alignment, use banded Smith-Waterman to create one.
|
|
|
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--- allpathslg-52488/src/pairwise_aligners/MatchList.cc
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+++ allpathslg-52488/src/pairwise_aligners/MatchList.cc
|
|
@@ -9,6 +9,8 @@
|
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|
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#include "pairwise_aligners/MatchList.h"
|
|
|
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+using std::max;
|
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+
|
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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"
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|
#include "paths/KmerPath.h"
|
|
|
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+using std::ostringstream;
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+using std::set;
|
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+
|
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// Function: AlignHyperKmerPath
|
|
//
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|
// 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"
|
|
|
|
-
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|
+using std::set;
|
|
|
|
/**
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|
* 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 @@
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#ifndef STLEXTENSIONS_H
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#define STLEXTENSIONS_H
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-using namespace std;
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-
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#include <functional>
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#include <vector>
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#include <bitset>
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@@ -21,6 +19,14 @@
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#include "feudal/BinaryStream.h"
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#include "system/StaticAssert.h"
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+using std::binary_function;
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+using std::unary_function;
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+using std::pair;
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+using std::bitset;
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+using std::initializer_list;
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+using std::vector;
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+using std::ostream;
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+
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/// minimum<T> is a function object.
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///
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/// If f is an object of class minimum<T> and x and y are objects of
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--- allpathslg-52488/src/system/MiscUtil.cc
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+++ allpathslg-52488/src/system/MiscUtil.cc
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@@ -21,6 +21,8 @@
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#include "system/HTMLUtils.h"
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#include "system/Utils.h"
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+using std::list;
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+
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static Bool makeOnlyIfNeeded = True;
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void SetMakeOnlyIfNeeded( Bool newMakeOnlyIfNeeded ) {
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--- allpathslg-52488/src/system/MiscUtil.h
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+++ allpathslg-52488/src/system/MiscUtil.h
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@@ -27,6 +27,9 @@
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#include "CommonSemanticTypes.h"
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#include "graph/Digraph.h"
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+using std::map;
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+using std::set;
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+
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// Semantic type: shellcmd_t
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// The name of a shell command.
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SemanticType( String, shellcmd_t );
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--- allpathslg-52488/src/system/ParsedArgs.cc
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+++ allpathslg-52488/src/system/ParsedArgs.cc
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@@ -26,6 +26,9 @@
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#include "system/HostName.h"
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#include "system/UseGDB.h"
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+using std::istrstream;
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+using std::mem_fun_ref;
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+
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#ifndef FatalErr
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#define FatalErr(message) { cout << message << endl << endl; exit(-1); }
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#endif
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--- allpathslg-52488/src/system/ParsedArgs.h
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+++ allpathslg-52488/src/system/ParsedArgs.h
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@@ -97,6 +97,8 @@
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#include "TokenizeString.h"
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#include "ParseSet.h"
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+using std::stringstream;
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+
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class parsed_arg_help {
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public:
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--- allpathslg-52488/src/system/ProcBuf.cc
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+++ allpathslg-52488/src/system/ProcBuf.cc
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@@ -15,6 +15,8 @@
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#include <sys/wait.h>
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#include <unistd.h>
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+using std::ios_base;
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+
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namespace
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{
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size_t const BUFFER_SIZE = 8192;
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--- allpathslg-52488/src/system/RunTime.cc
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+++ allpathslg-52488/src/system/RunTime.cc
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@@ -41,6 +41,10 @@
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#include <unwind.h>
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#endif
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+using std::strstream;
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+using std::hex;
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+using std::setw;
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+
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/// ===========================================================================
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///
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/// ReturnAddress(i), where 0 <= i <= 100: get the return address. The
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--- allpathslg-52488/src/system/RunTime.h
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+++ allpathslg-52488/src/system/RunTime.h
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@@ -14,6 +14,8 @@
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#include "system/Exit.h"
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#include "system/Types.h"
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+using std::ostream;
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+
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typedef void ArachneSignalHandler(int, siginfo_t*, void*);
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void arachne_signal_handler( int signal_number, siginfo_t* info, void* context,
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--- allpathslg-52488/src/system/System.cc
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+++ allpathslg-52488/src/system/System.cc
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@@ -36,6 +36,10 @@
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#include <dirent.h>
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+using std::istringstream;
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+using std::istream_iterator;
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+using std::ostringstream;
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+
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int SystemInternal( String command, const char *shell,
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int* pStatus, int* pErrNo )
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{
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@@ -1088,7 +1092,7 @@
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bool isReadable( String const& filename )
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{ ifstream ifs(filename.c_str());
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- return ifs; }
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+ return static_cast<bool>(ifs); }
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int Glob( const String& x, vector<String>& xs )
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{ glob_t globbuf;
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--- allpathslg-52488/src/system/System.h
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+++ allpathslg-52488/src/system/System.h
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@@ -21,6 +21,18 @@
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#include "system/Exit.h"
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#include "system/file/TempFile.h"
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+using std::vector;
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+using std::ostream;
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+using std::ofstream;
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+using std::ifstream;
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+using std::istream;
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+using std::ios;
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+using std::cout;
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+using std::flush;
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+using std::endl;
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+using std::setprecision;
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+using std::fixed;
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+
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#ifndef InputErr
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#define InputErr(message) \
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cout << "\nFatal error at " << Date() << ": " << message \
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--- allpathslg-52488/src/system/TraceVal.h
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+++ allpathslg-52488/src/system/TraceVal.h
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@@ -25,6 +25,9 @@
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#include "system/Assert.h"
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#include "system/Exit.h"
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+using std::cout;
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+using std::endl;
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+
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// Macros: Tracing macros
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// TRACEVAL_ON - undefine if you're not doing tracing
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// TRACEVAL_STOP_TRACING_COPIES -- call before an operation that shuffles
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--- allpathslg-52488/src/system/Types.h
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+++ allpathslg-52488/src/system/Types.h
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@@ -14,7 +14,7 @@
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#include <cstdlib>
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#include <netinet/in.h>
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-using namespace std;
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+
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// This assumes that all suns run Solaris...
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#if __sun == 1
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--- allpathslg-52488/src/system/WorklistUtils.cc
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+++ allpathslg-52488/src/system/WorklistUtils.cc
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@@ -32,6 +32,10 @@
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#include <sys/resource.h>
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#include <unistd.h>
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+using std::istringstream;
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+using std::istream_iterator;
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+using std::min;
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+
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namespace
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{
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pthread_t gMainThread;
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--- allpathslg-52488/src/util/FastaParser.cc
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+++ allpathslg-52488/src/util/FastaParser.cc
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@@ -22,6 +22,7 @@
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using std::string;
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using std::vector;
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+using std::istringstream;
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char* FastaParser::readLine()
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{
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--- allpathslg-52488/src/util/FastaParser.h
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+++ allpathslg-52488/src/util/FastaParser.h
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@@ -24,6 +24,8 @@
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#include <fstream>
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#include <vector>
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+using std::max;
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+
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/// Base class for the parsers for sequence, quality, and bits which follow.
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class FastaParser
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{
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--- allpathslg-52488/src/util/FastbStats.cc
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+++ allpathslg-52488/src/util/FastbStats.cc
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@@ -18,6 +18,8 @@
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#include "random/Random.h"
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+using std::map;
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+
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typedef VirtualMasterVec<BaseVec> VBaseVecVec;
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--- allpathslg-52488/src/util/Happening.cc
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+++ allpathslg-52488/src/util/Happening.cc
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@@ -25,6 +25,8 @@
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#include "FastIfstream.h"
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#include "MainTools.h"
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+using std::istringstream;
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+
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vec<String> tracebacks;
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Bool TALLYG;
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--- allpathslg-52488/src/util/MemMonitor.cc
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+++ allpathslg-52488/src/util/MemMonitor.cc
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@@ -21,7 +21,7 @@
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#include <signal.h>
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#include <time.h>
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-using namespace std;
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+using std::string;
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// convertion factors between jiffies and seconds (check your system!!!)
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const double sec_jif = 100.0;
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--- allpathslg-52488/src/util/Quala2Qualb.cc
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+++ allpathslg-52488/src/util/Quala2Qualb.cc
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@@ -11,6 +11,8 @@
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#include "FastIfstream.h"
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#include "Qualvector.h"
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+using std::istrstream;
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+
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int main(int argc, char *argv[])
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{
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RunTime();
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--- allpathslg-52488/src/util/QualbStats.cc
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+++ allpathslg-52488/src/util/QualbStats.cc
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@@ -20,6 +20,7 @@
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#include "Qualvector.h"
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#include "Basevector.h"
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+using std::scientific;
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#define NQ 256
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--- allpathslg-52488/src/util/ReadTrack.cc
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+++ allpathslg-52488/src/util/ReadTrack.cc
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@@ -33,6 +33,9 @@
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#include "util/ReadTracker.h"
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#include "util/RunCommand.h"
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+using std::map;
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+using std::set;
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+
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// Return filename portion of path (after last slash)
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String basename(const String path)
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{
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--- allpathslg-52488/src/util/ReadTracker.cc
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+++ allpathslg-52488/src/util/ReadTracker.cc
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@@ -11,6 +11,9 @@
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#include "VecUtilities.h"
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#include "util/ReadTracker.h"
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+using std::string;
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+using std::istringstream;
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+
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unsigned int
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ReadTracker::AddSource(String s)
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{
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--- allpathslg-52488/src/util/RunCommand.cc
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+++ allpathslg-52488/src/util/RunCommand.cc
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@@ -14,6 +14,8 @@
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#include <unistd.h>
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#include <sstream>
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+using std::ostringstream;
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+
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/**
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* RunCommand
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*/
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--- allpathslg-52488/src/util/TextTable.cc
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+++ allpathslg-52488/src/util/TextTable.cc
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@@ -13,6 +13,8 @@
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#include <sstream>
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#include <iterator>
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+using std::max;
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+
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vec<vec<String> > TextTable::GetTable( ) const {
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vec<vec<String> > table;
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for ( size_t i = 0; i < lines.size(); ++i ) {
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--- allpathslg-52488/src/util/TextTable.h
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+++ allpathslg-52488/src/util/TextTable.h
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@@ -33,6 +33,8 @@
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#include "Vec.h"
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#include "feudal/TrackingAllocator.h"
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+using std::string;
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+
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class TextTable {
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public:
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// == Special types to draw line and manipulate tables ==
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--- allpathslg-52488/src/Vec.h
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+++ allpathslg-52488/src/Vec.h
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@@ -50,6 +50,11 @@
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#include "Compare.h"
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#include "system/file/FileReader.h"
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+using std::numeric_limits;
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+using std::ostream_iterator;
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+using std::setfill;
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+using std::setw;
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+
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/////////////////////////////////////////////////////////////////////////////
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//
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// vec Class Declaration and Template Definitions
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--- allpathslg-52488/src/VecOverlap.cc
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+++ allpathslg-52488/src/VecOverlap.cc
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@@ -12,6 +12,9 @@
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#include "STLExtensions.h"
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#include <numeric>
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+using std::max;
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+using std::make_pair;
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+
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// Represents the suffix of the index'th word starting at the pos'th
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// character.
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template <class T>
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--- allpathslg-52488/src/VecUtilities.h
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+++ allpathslg-52488/src/VecUtilities.h
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@@ -37,6 +37,9 @@
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#include "Vec.h"
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#include <cstddef>
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+using std::less;
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+using std::equal_to;
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+using std::greater;
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/////////////////////////////////////////////////////////////////////////////
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//
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