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/*
This file is a part of KMC software distributed under GNU GPL 3 licence.
The homepage of the KMC project is http://sun.aei.polsl.pl/kmc
This file demonstrates the example usage of kmc_api software.
It reads kmer_counter's output and prints kmers to an output file.
Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot
Version: 2.3.0
Date : 2015-08-21
*/
#include "stdafx.h"
#include <iostream>
#include "../kmc_api/kmc_file.h"
#include "nc_utils.h"
void print_info(void);
int _tmain(int argc, char* argv[])
{
CKMCFile kmer_data_base;
int32 i;
uint32 min_count_to_set = 0;
uint32 max_count_to_set = 0;
std::string input_file_name;
std::string output_file_name;
FILE * out_file;
//------------------------------------------------------------
// Parse input parameters
//------------------------------------------------------------
if(argc < 3)
{
print_info();
return EXIT_FAILURE;
}
for(i = 1; i < argc; ++i)
{
if(argv[i][0] == '-')
{
if(strncmp(argv[i], "-ci", 3) == 0)
min_count_to_set = atoi(&argv[i][3]);
else if(strncmp(argv[i], "-cx", 3) == 0)
max_count_to_set = atoi(&argv[i][3]);
}
else
break;
}
if(argc - i < 2)
{
print_info();
return EXIT_FAILURE;
}
input_file_name = std::string(argv[i++]);
output_file_name = std::string(argv[i]);
if((out_file = fopen (output_file_name.c_str(),"wb")) == NULL)
{
print_info();
return EXIT_FAILURE;
}
setvbuf(out_file, NULL ,_IOFBF, 1 << 24);
//------------------------------------------------------------------------------
// Open kmer database for listing and print kmers within min_count and max_count
//------------------------------------------------------------------------------
if (!kmer_data_base.OpenForListing(input_file_name))
{
print_info();
return EXIT_FAILURE ;
}
else
{
uint32 _kmer_length;
uint32 _mode;
uint32 _counter_size;
uint32 _lut_prefix_length;
uint32 _signature_len;
uint32 _min_count;
uint64 _max_count;
uint64 _total_kmers;
kmer_data_base.Info(_kmer_length, _mode, _counter_size, _lut_prefix_length, _signature_len, _min_count, _max_count, _total_kmers);
//std::string str;
char str[1024];
uint32 counter_len;
CKmerAPI kmer_object(_kmer_length);
if(min_count_to_set)
if (!(kmer_data_base.SetMinCount(min_count_to_set)))
return EXIT_FAILURE;
if(max_count_to_set)
if (!(kmer_data_base.SetMaxCount(max_count_to_set)))
return EXIT_FAILURE;
if (_mode) //quake compatible mode
{
float counter;
while (kmer_data_base.ReadNextKmer(kmer_object, counter))
{
kmer_object.to_string(str);
str[_kmer_length] = '\t';
counter_len = CNumericConversions::Double2PChar(counter, 6, (uchar*)str + _kmer_length + 1);
str[_kmer_length + 1 + counter_len] = '\n';
fwrite(str, 1, _kmer_length + counter_len + 2, out_file);
}
}
else
{
uint64 counter;
while (kmer_data_base.ReadNextKmer(kmer_object, counter))
{
kmer_object.to_string(str);
str[_kmer_length] = '\t';
counter_len = CNumericConversions::Int2PChar(counter, (uchar*)str + _kmer_length + 1);
str[_kmer_length + 1 + counter_len] = '\n';
fwrite(str, 1, _kmer_length + counter_len + 2, out_file);
}
}
fclose(out_file);
kmer_data_base.Close();
}
return EXIT_SUCCESS;
}
// -------------------------------------------------------------------------
// Print execution options
// -------------------------------------------------------------------------
void print_info(void)
{
std::cout << "KMC dump ver. " << KMC_VER << " (" << KMC_DATE << ")\n";
std::cout << "\nUsage:\nkmc_dump [options] <kmc_database> <output_file>\n";
std::cout << "Parameters:\n";
std::cout << "<kmc_database> - kmer_counter's output\n";
std::cout << "Options:\n";
std::cout << "-ci<value> - print k-mers occurring less than <value> times\n";
std::cout << "-cx<value> - print k-mers occurring more of than <value> times\n";
};
// ***** EOF
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