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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_reader.h"
//************************************************************************************************************
// CBigKmerBinReader
//************************************************************************************************************
//----------------------------------------------------------------------------------
CBigKmerBinReader::CBigKmerBinReader(CKMCParams& Params, CKMCQueues& Queues)
{
tlbq = Queues.tlbq;
disk_logger = Queues.disk_logger;
bd = Queues.bd;
bbpq = Queues.bbpq;
sm_pmm_input_file = Queues.sm_pmm_input_file;
sm_mem_part_input_file = Params.sm_mem_part_input_file;
}
//----------------------------------------------------------------------------------
void CBigKmerBinReader::ProcessBigBin()
{
int32 bin_id;
CMemDiskFile *file;
string name;
uint64 size, n_rec, n_plus_x_recs, in_buffer, end_pos;
uint32 buffer_size, kmer_len;
uchar *file_buff, *tmp;
while (tlbq->get_next(bin_id))
{
bd->read(bin_id, file, name, size, n_rec, n_plus_x_recs, buffer_size, kmer_len);
cerr << "*";
file->Rewind();
end_pos = 0;
sm_pmm_input_file->reserve(file_buff);
while ( (in_buffer = end_pos + file->Read(file_buff + end_pos, 1, sm_mem_part_input_file - end_pos)) )
{
end_pos = 0;
for (; end_pos + 1 + (file_buff[end_pos] + kmer_len + 3) / 4 <= in_buffer; end_pos += 1 + (file_buff[end_pos] + kmer_len + 3) / 4);
uint64 rest = in_buffer - end_pos;
sm_pmm_input_file->reserve(tmp);
memcpy(tmp, file_buff + end_pos, rest);
bbpq->push(bin_id, file_buff, end_pos);
file_buff = tmp;
end_pos = rest;
}
sm_pmm_input_file->free(file_buff);
file->Close();
//Remove file
file->Remove();
disk_logger->log_remove(size);
}
bbpq->mark_completed();
}
//----------------------------------------------------------------------------------
CBigKmerBinReader::~CBigKmerBinReader()
{
}
//************************************************************************************************************
// CWBigKmerBinReader - wrapper for multithreading purposes
//************************************************************************************************************
//----------------------------------------------------------------------------------
// Constructor
CWBigKmerBinReader::CWBigKmerBinReader(CKMCParams& Params, CKMCQueues& Queues)
{
bkb_reader = new CBigKmerBinReader(Params, Queues);
}
//----------------------------------------------------------------------------------
// Destructor
CWBigKmerBinReader::~CWBigKmerBinReader()
{
delete bkb_reader;
}
//----------------------------------------------------------------------------------
// Execution
void CWBigKmerBinReader::operator()()
{
bkb_reader->ProcessBigBin();
}
// ***** EOF
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