Merge branch 'Smattr-63DADBC9-CFD6-4C2E-A70A-5EA771A3B770'

gatb-core/src/gatb/bank/impl/BankComposite.hpp

@@ -153,7 +153,7 @@ class BankComposite : public AbstractBank
     size_t getCompositionNb() { return _banks.size(); }
 
     /** \return maximum number of files. */
-    static const size_t getMaxNbFiles ()  { return 30; }
+    static size_t getMaxNbFiles ()  { return 30; }
 
     /** Return the vector of IBank objects.
      * \return the IBank objects. */

gatb-core/src/gatb/bank/impl/BankFasta.hpp

@@ -209,7 +209,7 @@ class BankFasta : public AbstractBank
 protected:
 
     /** \return maximum number of files. */
-    static const size_t getMaxNbFiles ()  { return 1; }
+    static size_t getMaxNbFiles ()  { return 1; }
 
     friend class Iterator;
 

gatb-core/src/gatb/bank/impl/BankRandom.hpp

@@ -81,7 +81,7 @@ class BankRandom : public AbstractBank
     void estimate (u_int64_t& number, u_int64_t& totalSize, u_int64_t& maxSize);
 
     /** \return maximum number of files. */
-    static const size_t getMaxNbFiles ()  { return 0; }
+    static size_t getMaxNbFiles ()  { return 0; }
 
     /************************************************************/
 

gatb-core/src/gatb/bank/impl/BankSplitter.hpp

@@ -99,7 +99,7 @@ class BankSplitter : public AbstractBank
     void estimate (u_int64_t& number, u_int64_t& totalSize, u_int64_t& maxSize);
 
     /** \return maximum number of files. */
-    static const size_t getMaxNbFiles ()  { return 0; }
+    static size_t getMaxNbFiles ()  { return 0; }
 
     /************************************************************/
 

gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp

@@ -119,7 +119,7 @@ class CountProcessorHistogram : public CountProcessorAbstract<span>
 				fprintf(histo2Dfile,"%5i:\t",ii);
 				for(int jj=0; jj<= _histogram->getLength2(); jj++)
 				{
-					fprintf(histo2Dfile,"\t%6lli", _histogram->get2D(ii,jj));
+					fprintf(histo2Dfile,"\t%6lli", (long long)_histogram->get2D(ii,jj));
 				}
 				fprintf(histo2Dfile,"\n");
 			}
@@ -134,7 +134,7 @@ class CountProcessorHistogram : public CountProcessorAbstract<span>
 			//output 1D histogram now
 			for(int ii=1; ii<= _histogram->getLength(); ii++)
 			{
-				fprintf(histo1Dfile,"%i\t%lli",ii,_histogram->get(ii));
+				fprintf(histo1Dfile,"%i\t%lli",ii,(long long)_histogram->get(ii));
 				fprintf(histo1Dfile,"\n");
 			}
 

gatb-core/src/gatb/tools/compression/HeaderCoder.cpp

@@ -25,6 +25,7 @@
 #define PRINT_DEBUG_ENCODER
 #define PRINT_DEBUG_DECODER
 */
+#include <string>
 
 
 //====================================================================================
@@ -703,13 +704,10 @@ void HeaderDecoder::decodeNumeric(){
 	u_int64_t value = CompressionUtils::decodeNumeric(_rangeDecoder, _numericModels[_misIndex]);
 	//_currentHeader += CompressionUtils::numberToString(value);
 
-	char temp[200];
-	snprintf(temp,200,"%llu",value);
-	_currentHeader += string(temp);
-	//_currentHeader += to_string(value); // C++11
+	_currentHeader += std::to_string(value);
 
 	#ifdef PRINT_DEBUG_DECODER
-		cout << "\t\t\tAdding: " << string(temp) << endl;
+		cout << "\t\t\tAdding: " << std::to_string(value) << endl;
 	#endif
 }
 
@@ -723,13 +721,10 @@ void HeaderDecoder::decodeDelta(){
 
 	value = CompressionUtils::getValueFromDelta(1, _prevFieldValues[_fieldIndex], value);
 
-	char temp[200];
-	snprintf(temp,200,"%llu",value);
-	_currentHeader += string(temp);
-	//_currentHeader += to_string(value);
+	_currentHeader += std::to_string(value);
 
 	#ifdef PRINT_DEBUG_DECODER
-		cout << "\t\t\tAdding: " << string(temp) << endl;
+		cout << "\t\t\tAdding: " << std::to_string(value) << endl;
 	#endif
 }
 
@@ -742,13 +737,10 @@ void HeaderDecoder::decodeDelta2(){
 	u_int64_t value = CompressionUtils::decodeNumeric(_rangeDecoder, _numericModels[_misIndex]);
 
 	value = CompressionUtils::getValueFromDelta(2, _prevFieldValues[_fieldIndex], value);
-	char temp[200];
-	snprintf(temp,200,"%llu",value);
-	_currentHeader += string(temp);
-	//_currentHeader += to_string(value);
+	_currentHeader += std::to_string(value);
 
 	#ifdef PRINT_DEBUG_DECODER
-		cout << "\t\t\tAdding: " << string(temp) << endl;
+		cout << "\t\t\tAdding: " << std::to_string(value) << endl;
 	#endif
 }
 

gatb-core/src/gatb/tools/compression/Leon.hpp

@@ -462,7 +462,7 @@ class BankLeon : public AbstractBank
 	void estimate (u_int64_t& number, u_int64_t& totalSize, u_int64_t& maxSize);
 
 	/** \return maximum number of files. */
-	static const size_t getMaxNbFiles ()  { return 0; }
+	static size_t getMaxNbFiles ()  { return 0; }
 
 	/************************************************************/
 

gatb-core/src/gatb/tools/math/Integer.hpp

@@ -114,7 +114,7 @@ class IntegerTemplate
     /** Get the size of an instance of the class used by the variant  (ie. one of the Ti template class parameters)
      * \return the size of an object (in bits).
      */
-    const size_t getSize ()         { return boost::apply_visitor (Integer_size(),  *(*this)); }
+    size_t getSize ()         { return boost::apply_visitor (Integer_size(),  *(*this)); }
 
     /** Get the HDF5 type for the the class used by the variant  (ie. one of the Ti template class parameters)
      * \param[in] isCompound : tells whether the type is composed or not
@@ -310,7 +310,7 @@ class IntegerTemplate
         template<typename T>  const char* operator() (const T& a) const { return a.getName();  }};
 
     struct Integer_size : public boost::static_visitor<const size_t>    {
-        template<typename T>  const size_t operator() (const T& a) const  { return a.getSize();  }};
+        template<typename T>  size_t operator() (const T& a) const  { return a.getSize();  }};
 
     struct Integer_plus : public boost::static_visitor<IntegerTemplate>    {
         template<typename T>              IntegerTemplate operator() (const T& a, const T& b) const  { return IntegerTemplate(a + b);  }

gatb-core/src/gatb/tools/math/LargeInt.hpp

@@ -137,7 +137,7 @@ template<int precision>  class LargeInt
     /** Get the size of an instance of the class
      * \return the size of an object (in bits).
      */
-    static const size_t getSize ()  { return 8*sizeof(u_int64_t)*precision; }
+    static size_t getSize ()  { return 8*sizeof(u_int64_t)*precision; }
 
     /********************************************************************************/
     /** Returns lower 64 bits */

gatb-core/src/gatb/tools/math/LargeInt1.pri

@@ -46,7 +46,7 @@ public:
 
     static const char* getName ()  { return "LargeInt<1>"; }
 
-    static const size_t getSize ()  { return 8*sizeof(u_int64_t); }
+    static size_t getSize ()  { return 8*sizeof(u_int64_t); }
 
     /** Returns lower 64 bits */
     u_int64_t toInt () const  {  return value;  }

gatb-core/src/gatb/tools/math/NativeInt64.hpp

@@ -59,7 +59,7 @@ class NativeInt64
      void setVal (u_int64_t c)  { value = c; }
 
 
-    static const size_t getSize ()  { return 8*sizeof(u_int64_t); }
+    static size_t getSize ()  { return 8*sizeof(u_int64_t); }
 
     NativeInt64 operator+  (const NativeInt64& other)   const   {  return value + other.value;  }
     NativeInt64 operator-  (const NativeInt64& other)   const   {  return value - other.value;  }

gatb-core/src/gatb/tools/math/NativeInt8.hpp

@@ -51,7 +51,7 @@ class NativeInt8 : private misc::ArrayData<u_int8_t, 1>
 
     static const char* getName ()  { return "NativeInt8"; }
 
-    static const size_t getSize ()  { return 8*sizeof(u_int8_t); }
+    static size_t getSize ()  { return 8*sizeof(u_int8_t); }
 
     operator char ()  const {  return (char) value[0];  }
 

gatb-core/thirdparty/BooPHF/BooPHF.h

@@ -4,6 +4,7 @@
 
 #pragma once
 #include <stdio.h>
+#include <cinttypes>
 #include <climits>
 #include <stdlib.h>
 #include <iostream>
@@ -836,7 +837,7 @@ we need this 2-functors scheme because HashFunctors won't work with unordered_ma
 
 			uint64_t totalsize =  totalsizeBitset +  _final_hash.size()*42*8 ;  // unordered map takes approx 42B per elem [personal test] (42B with uint64_t key, would be larger for other type of elem)
 
-			printf("Bitarray    %12llu  bits (%.2f %%)   (array + ranks )\n",
+			printf("Bitarray    %12" PRIu64 "  bits (%.2f %%)   (array + ranks )\n",
 				   totalsizeBitset, 100*(float)totalsizeBitset/totalsize);
 			printf("final hash  %12lu  bits (%.2f %%) (nb in final hash %lu)\n",
 				   _final_hash.size()*42*8, 100*(float)(_final_hash.size()*42*8)/totalsize,