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Compilation and code reuse improvements. #229

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Mar 7, 2024
Merged

Compilation and code reuse improvements. #229

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c02d4b2
Compilation and code reuse improvements.
maciejdlugosz Feb 20, 2024
193dd82
Keep reproducibility of a workflow.
maciejdlugosz Mar 5, 2024
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6 changes: 4 additions & 2 deletions kmc_CLI/kmc.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
#include <fstream>
#include <algorithm>
#include <iomanip>
#include <random>
using namespace std;

struct CLIParams
Expand Down Expand Up @@ -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"
Expand Down Expand Up @@ -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);

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10 changes: 5 additions & 5 deletions kmc_api/kmer_api.h
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Expand Up @@ -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;
Expand Down Expand Up @@ -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);
Expand All @@ -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;
Expand All @@ -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());
Expand Down
1 change: 1 addition & 0 deletions py_kmc_api/libs/pybind11/include/pybind11/attr.h
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Expand Up @@ -11,6 +11,7 @@
#pragma once

#include "cast.h"
#include <cstdint>

NAMESPACE_BEGIN(PYBIND11_NAMESPACE)

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