Merge pull request #229 from refresh-bio/compile_reuse

Compilation and code reuse improvements.
refresh-bio · Mar 7, 2024 · 65bff73 · 65bff73
2 parents d6c24dc + 193dd82
commit 65bff73
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Showing 3 changed files with 10 additions and 7 deletions.
diff --git a/kmc_CLI/kmc.cpp b/kmc_CLI/kmc.cpp
@@ -5,6 +5,7 @@
 #include <fstream>
 #include <algorithm>
 #include <iomanip>
+#include <random>
 using namespace std;
 
 struct CLIParams
@@ -36,7 +37,7 @@ void usage()
 		<< "  -sm - use strict memory mode (memory limit from -m<n> switch will not be exceeded)\n"
 		<< "  -hc - count homopolymer compressed k-mers (approximate and experimental)\n"
 		<< "  -p<par> - signature length (5, 6, 7, 8, 9, 10, 11); default: 9\n"
-		<< "  -f<a/q/m/bam/kmc> - input in FASTA format (-fa), FASTQ format (-fq), multi FASTA (-fm) or BAM (-fbam) or KMC(-fkmc); default: FASTQ\n"
+		<< "  -f<a/q/m/bam/kmc> - input in FASTA format (-fa), FASTQ format (-fq), multi FASTA (-fm) or BAM (-fbam) or KMC (-fkmc); default: FASTQ\n"
 		<< "  -ci<value> - exclude k-mers occurring less than <value> times (default: 2)\n"
 		<< "  -cs<value> - maximal value of a counter (default: 255)\n"
 		<< "  -cx<value> - exclude k-mers occurring more of than <value> times (default: 1e9)\n"
@@ -264,7 +265,8 @@ bool parse_parameters(int argc, char* argv[], Params& params)
 				input_file_names.push_back(s);
 
 		in.close();
-		std::random_shuffle(input_file_names.begin(), input_file_names.end());
+		std::mt19937 gen;
+		std::shuffle(input_file_names.begin(), input_file_names.end(), gen);
 	}
 	stage1Params.SetInputFiles(input_file_names);
 

diff --git a/kmc_api/kmer_api.h b/kmc_api/kmer_api.h
@@ -99,7 +99,7 @@ class CKmerAPI
 
 	// ----------------------------------------------------------------------------------
 	template<typename RandomAccessIterator>
-	inline void to_string_impl(RandomAccessIterator iter)
+	inline void to_string_impl(RandomAccessIterator iter) const
 	{
 		uchar *byte_ptr;
 		uchar c;
@@ -431,7 +431,7 @@ class CKmerAPI
 	// Convert kmer into string (an alphabet ACGT)
 	// RET	: string kmer
 	//-----------------------------------------------------------------------
-	inline std::string to_string()
+	inline std::string to_string() const
 	{
 		std::string string_kmer;		
 		string_kmer.resize(kmer_length);
@@ -442,14 +442,14 @@ class CKmerAPI
 	// Convert kmer into string (an alphabet ACGT). The function assumes enough memory was allocated
 	// OUT	: str - string kmer. 
 	//-----------------------------------------------------------------------
-	inline void to_string(char *str)
+	inline void to_string(char *str) const
 	{
 		to_string_impl(str);
 		str[kmer_length] = '\0';
 	};
 
 
-	inline void to_long(std::vector<uint64>& kmer)
+	inline void to_long(std::vector<uint64>& kmer) const
 	{
 		kmer.resize(no_of_rows);
 		uint32 offset = 62 - ((kmer_length - 1 + byte_alignment) & 31) * 2;
@@ -473,7 +473,7 @@ class CKmerAPI
 	// Convert kmer into string (an alphabet ACGT)
 	// OUT 	: str - string kmer
 	//-----------------------------------------------------------------------
-	inline void to_string(std::string &str)
+	inline void to_string(std::string &str) const
 	{	
 		str.resize(kmer_length);
 		to_string_impl(str.begin());

diff --git a/py_kmc_api/libs/pybind11/include/pybind11/attr.h b/py_kmc_api/libs/pybind11/include/pybind11/attr.h
@@ -11,6 +11,7 @@
 #pragma once
 
 #include "cast.h"
+#include <cstdint>
 
 NAMESPACE_BEGIN(PYBIND11_NAMESPACE)