Description: fix spelling 
Author: Sascha Steinbiss <sascha@steinbiss.name> 
Applied-Upstream: https://github.com/marekkokot/KMC/pull/8 
--- a/kmc_tools/config.h
+++ b/kmc_tools/config.h
@@ -243,11 +243,11 @@ public:
 		std::cout << "  sort                - sorts k-mers from database generated by KMC2.x\n";
 		std::cout << "  reduce              - exclude too rare and too frequent k-mers\n";
 		std::cout << "  compact             - remove counters (store only k-mers)\n";
-		std::cout << "  histogram           - histogram of k-mers occurences\n";
+		std::cout << "  histogram           - histogram of k-mers occurrences\n";
 		std::cout << "  dump                - dump k-mers and counters to text file\n";		
 		std::cout << " more complex operations:\n";
 		std::cout << "  complex             - complex operations with a number of input databases\n";
-		std::cout << " other operatations:\n";
+		std::cout << " other operations:\n";
 		std::cout << "  filter              - filter out reads with too small number of k-mers\n";
 		std::cout << " global parameters:\n";
 		std::cout << "  -t<value>           - total number of threads (default: no. of CPU cores)\n";
@@ -301,7 +301,7 @@ public:
 	void Display() const override
 	{
 		Display2ArgGeneral();
-		std::cout << "The output database will contains only k-mers that are present in first input set and have counters higher than apropriate k - mers in second set. For each k - mer the counter is equal to difference between counter in first set and counter in second set.";
+		std::cout << "The output database will contains only k-mers that are present in first input set and have counters higher than appropriate k - mers in second set. For each k - mer the counter is equal to difference between counter in first set and counter in second set.";
 		std::cout << "Example:\n";
 		std::cout << "kmc -k28 file1.fastq kmers1 tmp\n";
 		std::cout << "kmc -k28 file2.fastq kmers2 tmp\n";
@@ -332,7 +332,7 @@ public:
 	{}
 	void Display() const override
 	{
-		std::cout << "Complex operation allows to define operations for more than 2 input k-mers sets. Command-line syntax:\n";
+		std::cout << "Complex operation allows one to define operations for more than 2 input k-mers sets. Command-line syntax:\n";
 		std::cout << "kmc_tools complex <operations_definition_file>\n";
 		std::cout << " operations_definition_file - path to file which define input sets and operations. It is text file with following syntax:\n";
 		std::cout << " __________________________________________________________________ \n";
@@ -355,7 +355,7 @@ public:
 		std::cout << "out_db_path - path to output database\n";
 		std::cout << "ref_input - one of input1, input2, ..., inputN\n";
 		std::cout << "oper - one of {*,-,~,+}, which refers to {intersect, kmers_subtract, counters_subtract, union}\n";
-		std::cout << "operator * has the highest priority. Other operators has equals priorities. Order of operations can be changed with barenthesis\n";
+		std::cout << "operator * has the highest priority. Other operators has equals priorities. Order of operations can be changed with parentheses\n";
 		std::cout << "output_params are:\n";
 		std::cout << "  -ci<value> - exclude k-mers occurring less than <value> times \n";
 		std::cout << "  -cx<value> - exclude k-mers occurring more of than <value> times\n";
@@ -547,4 +547,4 @@ public:
 #endif
 
 
-// ***** EOF
\ No newline at end of file
+// ***** EOF
--- a/kmer_counter/bkb_sorter.h
+++ b/kmer_counter/bkb_sorter.h
@@ -367,7 +367,7 @@ template<unsigned SIZE> void CBigKmerBin
 }
 
 //----------------------------------------------------------------------------------
-//Binary search position of first occurence of symbol 'symb' in [start_pos,end_pos). Offset defines which symbol in k+x-mer is taken.
+//Binary search position of first occurrence of symbol 'symb' in [start_pos,end_pos). Offset defines which symbol in k+x-mer is taken.
 template <unsigned SIZE> uint64 CBigKmerBinSorter_Impl<CKmer<SIZE>, SIZE>::FindFirstSymbOccur(CBigKmerBinSorter<CKmer<SIZE>, SIZE> &ptr, uint64 start_pos, uint64 end_pos, uint32 offset, uchar symb)
 {
 	uint32 kxmer_offset = (ptr.kmer_len + ptr.max_x - offset) * 2;
--- a/kmer_counter/kb_sorter.h
+++ b/kmer_counter/kb_sorter.h
@@ -830,7 +830,7 @@ template <typename KMER_T, unsigned SIZE
 }
 
 //----------------------------------------------------------------------------------
-//Binary search position of first occurence of symbol 'symb' in [start_pos,end_pos). Offset defines which symbol in k+x-mer is taken.
+//Binary search position of first occurrence of symbol 'symb' in [start_pos,end_pos). Offset defines which symbol in k+x-mer is taken.
 template <unsigned SIZE> uint64 CKmerBinSorter_Impl<CKmer<SIZE>, SIZE>::FindFirstSymbOccur(CKmerBinSorter<CKmer<SIZE>, SIZE> &ptr, uint64 start_pos, uint64 end_pos, uint32 offset, uchar symb)
 {
 	uint32 kxmer_offset = (ptr.kmer_len + ptr.max_x - offset) * 2;
--- a/kmer_counter/s_mapper.h
+++ b/kmer_counter/s_mapper.h
@@ -30,12 +30,12 @@ class CSignatureMapper
 
 	class Comp
 	{
-		uint32* signature_occurences;
+		uint32* signature_occurrences;
 	public:
-		Comp(uint32* _signature_occurences) : signature_occurences(_signature_occurences){}
+		Comp(uint32* _signature_occurrences) : signature_occurrences(_signature_occurrences){}
 		bool operator()(int i, int j)
 		{
-			return signature_occurences[i] > signature_occurences[j];
+			return signature_occurrences[i] > signature_occurrences[j];
 		}
 	};
 	
--- a/kmc_tools/kmc1_db_writer.h
+++ b/kmc_tools/kmc1_db_writer.h
@@ -37,7 +37,7 @@ public:
 		{
 			if (fwrite(buf, 1, size, kmc_suf) != size)
 			{
-				std::cout << "Error while writting to kmc_suf file\n";
+				std::cout << "Error while writing to kmc_suf file\n";
 				exit(1);
 			}
 			delete[] buf;
@@ -78,9 +78,9 @@ private:
 
 	void store_pre_buf();
 	void send_suf_buf_to_queue();
-	void start_writting();
+	void start_writing();
 	inline void add_kmer(CKmer<SIZE>& kmer, uint32 counter);
-	void finish_writting();	
+	void finish_writing();	
 
 	template<typename T> void write_header_part(T data);
 	void calc_lut_prefix_len();
@@ -159,7 +159,7 @@ template <unsigned SIZE> CKMC1DbWriter<S
 template<unsigned SIZE> bool CKMC1DbWriter<SIZE>::Process()
 {
 
-	start_writting();
+	start_writing();
 
 	//Converts bundles to output buffers, sufix buffer is placed to another queue and write in separate thread (sufix_writer)
 	std::thread preparing_thread([this]{
@@ -201,7 +201,7 @@ template<unsigned SIZE> bool CKMC1DbWrit
 	preparing_thread.join();
 	suf_buf_writing_thread.join();
 
-	finish_writting();
+	finish_writing();
 	return true;
 }
 
@@ -232,22 +232,22 @@ template <unsigned SIZE> template <typen
 }
 
 /*****************************************************************************************************************************/
-template<unsigned SIZE> void CKMC1DbWriter<SIZE>::start_writting()
+template<unsigned SIZE> void CKMC1DbWriter<SIZE>::start_writing()
 {
 	if (fwrite("KMCP", 1, 4, kmc_pre) != 4)
 	{
-		std::cout << "Error while writting starting KMCP marker";
+		std::cout << "Error while writing starting KMCP marker";
 		exit(1);
 	}
 	if (fwrite("KMCS", 1, 4, kmc_suf) != 4)
 	{
-		std::cout << "Error while writting starting KMCS marker";
+		std::cout << "Error while writing starting KMCS marker";
 		exit(1);
 	}
 }
 
 /*****************************************************************************************************************************/
-template<unsigned SIZE> void CKMC1DbWriter<SIZE>::finish_writting()
+template<unsigned SIZE> void CKMC1DbWriter<SIZE>::finish_writing()
 {
 	uint32 max_prefix = (1 << 2 * lut_prefix_len);
 	while (current_prefix < max_prefix - 1)
@@ -284,12 +284,12 @@ template<unsigned SIZE> void CKMC1DbWrit
 
 	if (fwrite("KMCP", 1, 4, kmc_pre) != 4)
 	{
-		std::cout << "Error while writting end KMCP marker";
+		std::cout << "Error while writing end KMCP marker";
 		exit(1);
 	}
 	if (fwrite("KMCS", 1, 4, kmc_suf) != 4)
 	{
-		std::cout << "Error while writting end KMCS marker";
+		std::cout << "Error while writing end KMCS marker";
 		exit(1);
 	}
 	fclose(kmc_pre);
@@ -327,7 +327,7 @@ template<unsigned SIZE> void CKMC1DbWrit
 {	
 	if (fwrite(pre_buff, sizeof(uint64), pre_pos, kmc_pre) != pre_pos)
 	{
-		std::cout << "Error while writting to kmc_pre file\n";
+		std::cout << "Error while writing to kmc_pre file\n";
 		exit(1);
 	}
 	pre_pos = 0;
--- a/kmer_counter/radix.cpp
+++ b/kmer_counter/radix.cpp
@@ -143,7 +143,7 @@ void RadixSort_uint8(uint32 *&data_ptr,
   Satish, N., Kim, C., Chhugani, J., Nguyen, A.D., Lee, V.W., Kim, D., Dubey, P. (2010). 
   Fast Sort on CPUs and GPUs. A Case for Bandwidth Oblivious SIMD Sort. 
   Proc. of the 2010 Int. Conf. on Management of data, pp. 351362. 
-  The usage of software-managed buffers in the writting phase results in diminishing
+  The usage of software-managed buffers in the writing phase results in diminishing
   the influence of irregular memory accesses. As the number of cache conflict misses
   is reduced better efficiency is reached.*/
 template<typename COUNTER_TYPE, typename INT_TYPE>
--- a/kmc_tools/kmc2_db_reader.h
+++ b/kmc_tools/kmc2_db_reader.h
@@ -869,7 +869,7 @@ template<unsigned SIZE> CKMC2DbReaderSor
 	my_fseek(kmc_pre, 4, SEEK_SET);
 	if (fread(LUTS, sizeof(uint64), lut_recs, kmc_pre) != lut_recs)
 	{
-		std::cout << "Some error occured while reading LUTS from kmc2 prefix file \n";
+		std::cout << "Some error occurred while reading LUTS from kmc2 prefix file \n";
 		exit(1);
 	}
 	fclose(kmc_pre);
@@ -1005,7 +1005,7 @@ template<unsigned SIZE> CKMC2DbReaderSor
 //	my_fseek(kmc_suf, start, SEEK_SET);
 //	if (fread(buf, 1, size, kmc_suf) != size)
 //	{
-//		std::cout << "Error: some error occured while reading " << desc.file_src << ".kmc_suf file\n";
+//		std::cout << "Error: some error occurred while reading " << desc.file_src << ".kmc_suf file\n";
 //		exit(1);
 //	}
 //#ifdef ENABLE_LOGGER
@@ -1336,7 +1336,7 @@ template<unsigned SIZE> CKMC2DbReader<SI
 		db_reader_counters_only = std::make_unique<CKMC2DbReaderCountersOnly<SIZE>>(header, desc);
 		break;
 	default: //should never be here
-		std::cout << "Error: unknow open mode \n";
+		std::cout << "Error: unknown open mode \n";
 		exit(1);
 	}
 }
@@ -1395,4 +1395,4 @@ template<unsigned SIZE> bool CKMC2DbRead
 
 
 
-#endif
\ No newline at end of file
+#endif
--- a/kmc_tools/parameters_parser.cpp
+++ b/kmc_tools/parameters_parser.cpp
@@ -140,7 +140,7 @@ void CParametersParser::read_input_fastq
 				config.filtering_params.input_file_type = CFilteringParams::file_type::fastq;
 				break;
 			default:
-				cout << "Error: unknow parameter " << argv[pos - 1] << "\n";
+				cout << "Error: unknown parameter " << argv[pos - 1] << "\n";
 				exit(1);
 				break;
 			}
@@ -207,7 +207,7 @@ void CParametersParser::read_dump_params
 		}
 		else
 		{
-			cout << "Warning: Unknow parameter for dump operation: " << argv[pos] << "\n";			
+			cout << "Warning: Unknown parameter for dump operation: " << argv[pos] << "\n";			
 		}
 		++pos;
 	}
@@ -242,7 +242,7 @@ void CParametersParser::read_input_desc(
 		}
 		else
 		{
-			cout << "Error: Unknow parameter: " << argv[pos];
+			cout << "Error: Unknown parameter: " << argv[pos];
 			exit(1);
 		}
 	}
@@ -279,7 +279,7 @@ void CParametersParser::read_output_desc
 		}
 		else
 		{
-			cout << "Error: Unknow parameter: " << argv[pos];
+			cout << "Error: Unknown parameter: " << argv[pos];
 			exit(1);
 		}
 	}
@@ -355,7 +355,7 @@ void CParametersParser::Parse()
 	}
 	else
 	{
-		cout << "Error: Unknow mode: " << argv[pos] << "\n";
+		cout << "Error: Unknown mode: " << argv[pos] << "\n";
 		Usage();
 		exit(1);
 	}
@@ -533,4 +533,4 @@ void CParametersParser::SetThreads()
 
 
 
-// ***** EOF
\ No newline at end of file
+// ***** EOF
--- a/kmc_tools/parameters_parser.h
+++ b/kmc_tools/parameters_parser.h
@@ -67,7 +67,7 @@ CExpressionNode<SIZE>* CParametersParser
 			expression_root = new CCountersSubtractionNode<SIZE>;
 			break;
 		default:
-			std::cout << "Error: unknow operation\n";
+			std::cout << "Error: unknown operation\n";
 			exit(1);
 		}
 		expression_root->AddLeftChild(left);
@@ -98,7 +98,7 @@ CExpressionNode<SIZE>* CParametersParser
 	}
 	else //should never be here
 	{
-		std::cout << "Error: unknow operation\n";
+		std::cout << "Error: unknown operation\n";
 #ifdef ENABLE_DEBUG
 		std::cout << __FUNCTION__ << " line: " << __LINE__ << "\n";
 #endif
@@ -108,4 +108,4 @@ CExpressionNode<SIZE>* CParametersParser
 #endif
 
 
-// ***** EOF
\ No newline at end of file
+// ***** EOF
--- a/kmc_tools/parser.cpp
+++ b/kmc_tools/parser.cpp
@@ -115,7 +115,7 @@ void CParser::parseInputLine(const std::
 					desc.cutoff_max = atoi(tmp.c_str() + 3);
 					continue;
 				}
-				std::cout << "Error: Unknow parameter " << tmp << " for variable " << match[1] << ", line: "<< line_no <<"\n";
+				std::cout << "Error: Unknown parameter " << tmp << " for variable " << match[1] << ", line: "<< line_no <<"\n";
 				exit(1);
 			}
 
@@ -160,7 +160,7 @@ void CParser::parseOtuputParamsLine()
 				config.output_desc.counter_max = atoi(tmp.c_str() + 3);
 				continue;
 			}
-			std::cout << "Error: Unknow parameter " << tmp << " for variable " << tmp << ", line: " << line_no << "\n";
+			std::cout << "Error: Unknown parameter " << tmp << " for variable " << tmp << ", line: " << line_no << "\n";
 			exit(1);
 		}
 	}
