Wrap kmc_tools to a namespace to fix linking conflicts

kmc_tools/bundle.h

@@ -10,10 +10,13 @@
 
 #ifndef _BUNDLE_H
 #define _BUNDLE_H
+
 #include "config.h"
 #include "defs.h"
 #include "kmer.h"
 
+namespace kmc_tools{
+
 //************************************************************************************************************
 // CBundle and CInput are CORE classes of this application. CInputs are nodes of binary tree which 
 // represent operations. Leafs of this tree are kmc database (1 or 2) inputs (sets of k-mers).
@@ -332,6 +335,8 @@ template<unsigned SIZE> inline bool CBundle<SIZE>::Finished()
  return false;
 }
 
+} // namespace
+
 #endif
 
 

kmc_tools/check_kmer.h

@@ -16,6 +16,8 @@
 #include "../kmc_api/mmer.h"
 #include <string>
 
+namespace kmc_tools{
+
 template<unsigned SIZE>
 class CKmerCheck
 {
@@ -402,4 +404,6 @@ class CKmerCheckKFF
  }
 };
 
+} // namespace
+
 #endif

kmc_tools/config.h

@@ -19,6 +19,8 @@
 #include "kmer_file_header.h"
 #include "percent_progress.h"
 
+namespace kmc_tools{
+
 enum class CounterOpType { MIN, MAX, SUM, DIFF, FROM_DB1, FROM_DB2, NONE };
 enum class OutputType { KMC1, KFF1 };
 enum class KmerDBOpenMode { sequential, sorted, counters_only };
@@ -497,6 +499,8 @@ class CUsageDisplayerFactory
  }
 };
 
+} // namespace
+
 #endif
 
 

kmc_tools/db_reader_factory.h

@@ -7,6 +7,8 @@
 #include "kmc2_db_reader.h"
 #include "kff_db_reader.h"
 
+namespace kmc_tools{
+
 template<unsigned SIZE>
 CInput<SIZE>* db_reader_factory(const CKmerFileHeader& header, const CInputDesc& input_desc, KmerDBOpenMode kmer_db_open_mode)
 {
@@ -26,6 +28,8 @@ CInput<SIZE>* db_reader_factory(const CKmerFileHeader& header, const CInputDesc&
  }
 }
 
+} // namespace
+
 #endif // !_DB_READER_FACTORY_H
 
 

kmc_tools/db_writer.h

@@ -12,6 +12,8 @@ Date : 2023-03-10
 #define _DB_WRITER_H
 #include "bundle.h"
 
+namespace kmc_tools{
+
 template<unsigned SIZE>
 class CDbWriter
 {
@@ -23,4 +25,6 @@ class CDbWriter
  virtual void MultiOptputFinish() = 0;
  virtual ~CDbWriter() = default;
 };
+
+} // namespace
 #endif

kmc_tools/db_writer_factory.h

@@ -4,6 +4,8 @@
 #include "kmc1_db_writer.h"
 #include "kff_db_writer.h"
 
+namespace kmc_tools{
+
 template<unsigned SIZE>
 CDbWriter<SIZE>* db_writer_factory(COutputDesc& output_desc, CBundle<SIZE>* bundle = nullptr)
 {
@@ -21,5 +23,5 @@ CDbWriter<SIZE>* db_writer_factory(COutputDesc& output_desc, CBundle<SIZE>* bund
  }
 }
 
-
+} // namespace
 #endif

kmc_tools/defs.h

@@ -16,6 +16,8 @@
 
 #include <cinttypes>
 
+namespace kmc_tools{
+
 using uint32 = uint32_t;
 using uint64 = uint64_t;
 using int32 = int32_t;
@@ -108,6 +110,8 @@ using uchar = unsigned char;
  val = (val<<24) | ((val<<8) & 0x00ff0000) | ((val >> 8) & 0x0000ff00) | (val >> 24);
 #endif
 
+} // namespace
+
 #endif
 
 

kmc_tools/develop.h

@@ -8,6 +8,8 @@
 #include "defs.h"
 #include "timer.h"
 
+namespace kmc_tools{
+
 #ifdef ENABLE_LOGGER
 
 
@@ -62,5 +64,7 @@ class CLoger
 };
 #endif
 
+} // namespace
+
 
 #endif

kmc_tools/dump_writer.h

@@ -16,6 +16,8 @@
 #include "config.h"
 #include <fstream>
 
+namespace kmc_tools{
+
 
 //wrapper to simplify interface
 
@@ -249,4 +251,6 @@ class CDumpWriterForTransform : public CDumpWriterBase<SIZE>
  }
 };
 
+} // namespace
+
 #endif

kmc_tools/expression_node.h

@@ -18,6 +18,8 @@
 #include <memory>
 #include "db_reader_factory.h"
 
+namespace kmc_tools{
+
 //************************************************************************************************************
 // CExpressionNode - Base abstract class representing expression node. In first stage of algorithm from
 // user input there is created binary tree. Node type represents operation. This tree is only for generating
@@ -215,6 +217,8 @@ template<unsigned SIZE> class CInputNode : public CExpressionNode<SIZE>
 #endif
 };
 
+} // namespace
+
 
 #endif
 

kmc_tools/fastq_filter.cpp

@@ -11,6 +11,7 @@ Date : 2023-03-10
 #include "fastq_filter.h"
 #include <numeric>
 
+using namespace kmc_tools;
 using namespace std;
 
 /*****************************************************************************************************************************/

kmc_tools/fastq_filter.h

@@ -16,6 +16,8 @@ Date : 2023-03-10
 
 #include "kff_random_access.h"
 
+namespace kmc_tools{
+
 //************************************************************************************************************
 // CFastqFilter - filter of reads
 //************************************************************************************************************
@@ -100,6 +102,8 @@ class CWFastqFilter
  void operator()();
 };
 
+} // namespace
+
 
 #endif
 

kmc_tools/fastq_reader.cpp

@@ -14,6 +14,8 @@
 #include "defs.h"
 #include "fastq_reader.h"
 
+using namespace kmc_tools;
+
 //************************************************************************************************************
 // CFastqReader - reader class
 //************************************************************************************************************

kmc_tools/fastq_reader.h

@@ -19,6 +19,8 @@
 
 #include "../3rd_party/cloudflare/zlib.h"
 
+namespace kmc_tools{
+
 using namespace std;
 
 
@@ -87,6 +89,8 @@ class CWFastqReaderKMCTools { // Jarno Alanko 12.5.2022: Appended KMCTools to na
  void operator()();
 };
 
+} // namespace
+
 #endif
 
 // ***** EOF

kmc_tools/fastq_writer.cpp

@@ -10,6 +10,9 @@
 
 #include "fastq_writer.h"
 #include <iostream>
+
+using namespace kmc_tools;
+
 using namespace std;
 
 

kmc_tools/fastq_writer.h

@@ -16,6 +16,8 @@
 #include "queues.h"
 #include <string>
 
+namespace kmc_tools{
+
 //************************************************************************************************************
 // CFastqWriter - Writer of fastq/fasta file
 //************************************************************************************************************
@@ -40,5 +42,7 @@ class CWFastqWriter
  void operator()();
 };
 
+} // namespace
+
 #endif
 

kmc_tools/histogram_writer.h

@@ -16,6 +16,7 @@
 #include <vector>
 #include <fstream>
 
+namespace kmc_tools{
 
 class CHistogramWriterBase
 {
@@ -106,4 +107,6 @@ class CHistogramWriterForTransform : public CHistogramWriterBase
  }
 };
 
+} // namespace
+
 #endif

kmc_tools/kff_db_reader.h

@@ -13,6 +13,8 @@
 #include <memory>
 #include <algorithm>
 
+namespace kmc_tools{
+
 //TODO KFF: consider minimizers sections
 
 //Forward declaration
@@ -1491,4 +1493,6 @@ class CKFFDbReaderSeq
  }
 };
 
+} // namespace
+
 #endif

kmc_tools/kff_db_writer.h

@@ -16,6 +16,7 @@ Date : 2023-03-10
 #include "../kmc_core/kff_writer.h"
 #include "defs.h"
 
+namespace kmc_tools{
 
 template<unsigned SIZE> class CKFFDbWriter : public CDbWriter<SIZE>
 {
@@ -148,4 +149,6 @@ template<unsigned SIZE> class CKFFDbWriter : public CDbWriter<SIZE>
  }
 };
 
+} // namespace
+
 #endif

kmc_tools/kff_info_reader.cpp

@@ -7,6 +7,8 @@
 #include <algorithm>
 #include <cstring>
 
+using namespace kmc_tools;
+
 std::string CKFFInfoReader::ReadVarName()
 {
  std::string res;

kmc_tools/kff_info_reader.h

@@ -5,6 +5,7 @@
 #include <string>
 #include <map>
 
+namespace kmc_tools{
 
 template<typename T>
 void LoadBigEndian(const uint8_t* buff, T& data)
@@ -85,3 +86,5 @@ class CKFFInfoReader
 
  ~CKFFInfoReader();
 };
+
+} // namespace

kmc_tools/kff_kmc2_reader_utils.h

@@ -15,6 +15,8 @@ Date : 2023-03-10
 #include <mutex>
 #include <thread>
 
+namespace kmc_tools{
+
 //************************************************************************************************************
 // CParentSubthreadSynchronizer - Synchronize subthreads created by CMergerParent
 //************************************************************************************************************
@@ -115,4 +117,6 @@ class CParentSubthreadDescQueue
  }
 };
 
+} // namespace
+
 #endif

kmc_tools/kff_random_access.h

@@ -18,6 +18,8 @@
 #include "db_reader_factory.h"
 #include "../kmc_api/kmc_file.h"
 
+namespace kmc_tools{
+
 class CKffAndKMCRandomAccess : protected CKMCFile
 {
  uint32_t suffix_bits;
@@ -168,6 +170,8 @@ class CKffAndKMCRandomAccess : protected CKMCFile
  }
 };
 
+} // namespace
+
 #endif //_KFF_RANDOM_ACCESS_H
 
 

kmc_tools/kmc1_db_reader.h

@@ -21,6 +21,8 @@ Date : 2023-03-10
 #include <thread>
 #include <tuple>
 
+namespace kmc_tools{
+
 //I'm going to read a little after buffer, this will be always correctly ignored, but reading itself is illegal
 //using 16 because 8 of Ckmer, and possibly 8 for counter
 #define SUFFIX_BUFF_EXTRA_BYTES 16
@@ -716,7 +718,7 @@ template<unsigned SIZE> bool CKMC1DbReader<SIZE>::fill_bundle()
  return false;
 }
 
-
+} // namespace
 #endif
 
 // ***** EOF