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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
Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot
Version: 3.1.1
Date : 2019-05-19
*/
#include "stdafx.h"
#include "bkb_writer.h"
//************************************************************************************************************
// CBigKmerBinWriter
//************************************************************************************************************
//----------------------------------------------------------------------------------
CBigKmerBinWriter::CBigKmerBinWriter(CKMCParams& Params, CKMCQueues& Queues)
{
disk_logger = Queues.disk_logger;
bbspq = Queues.bbspq;
sm_pmm_sorter_suffixes = Queues.sm_pmm_sorter_suffixes;
sm_pmm_sorter_lut = Queues.sm_pmm_sorter_lut;
working_directory = Params.working_directory;
bbd = Queues.bbd;
sm_cbc = Queues.sm_cbc;
}
//----------------------------------------------------------------------------------
void CBigKmerBinWriter::Process()
{
int32 curr_bin_id = -1;
uchar* suff_buff = nullptr;
uint64 suff_buff_size;
uint64* lut = nullptr;
uint64 lut_size = 0;
bool last_one_in_sub_bin;
bool first_in_sub_bin = true;
FILE* file = nullptr;
string name;
uint64 file_size = 0;
while (bbspq->pop(bin_id, sub_bin_id, suff_buff, suff_buff_size, lut, lut_size, last_one_in_sub_bin))
{
if (curr_bin_id != bin_id)
{
if (curr_bin_id != -1)
sm_cbc->push(curr_bin_id);
curr_bin_id = bin_id;
}
if (first_in_sub_bin)
{
file_size = 0;
name = GetName();
file = fopen(name.c_str(), "wb+");
if (!file)
{
cerr << "Error: can not open file : " << name;
exit(1);
}
setbuf(file, nullptr);
}
first_in_sub_bin = false;
if (suff_buff_size)
{
disk_logger->log_write(suff_buff_size);
if (fwrite(suff_buff, 1, suff_buff_size, file) != suff_buff_size)
{
cerr << "Error while writing to file : " << name;
exit(1);
}
file_size += suff_buff_size;
sm_pmm_sorter_suffixes->free(suff_buff);
}
if (lut_size)
{
disk_logger->log_write(lut_size * sizeof(uint64));
if (fwrite(lut, sizeof(uint64), lut_size, file) != lut_size)
{
cerr << "Error while writing to file : " << name;
exit(1);
}
file_size += lut_size * sizeof(uint64);
sm_pmm_sorter_lut->free((uchar*)lut);
}
if (last_one_in_sub_bin)
{
bbd->push(bin_id, sub_bin_id, 0, 0, file, name, file_size);
first_in_sub_bin = true;
}
}
if(curr_bin_id != -1)
sm_cbc->push(curr_bin_id);
sm_cbc->mark_completed();
}
//----------------------------------------------------------------------------------
string CBigKmerBinWriter::GetName()
{
string s_tmp = std::to_string(bin_id);
while (s_tmp.length() < 5)
s_tmp = string("0") + s_tmp;
string s1 = std::to_string(sub_bin_id);
while (s1.length() < 3)
s1 = string("0") + s1;
if (*working_directory.rbegin() != '/' && *working_directory.rbegin() != '\\')
working_directory += "/";
return working_directory + "kmc_" + s_tmp + "_" + s1 + "_" + s1 + ".bin";
}
//************************************************************************************************************
// CWBigKmerBinWriter - wrapper for multithreading purposes
//************************************************************************************************************
//----------------------------------------------------------------------------------
// Constructor
CWBigKmerBinWriter::CWBigKmerBinWriter(CKMCParams& Params, CKMCQueues& Queues)
{
bkb_writer = new CBigKmerBinWriter(Params, Queues);
}
//----------------------------------------------------------------------------------
// Destructor
CWBigKmerBinWriter::~CWBigKmerBinWriter()
{
delete bkb_writer;
}
//----------------------------------------------------------------------------------
// Execution
void CWBigKmerBinWriter::operator()()
{
bkb_writer->Process();
}
// ***** EOF
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