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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: Marek Kokot
Version: 3.2.4
Date : 2024-02-09
*/
#ifndef _FASTQ_FILTER_H
#define _FASTQ_FILTER_H
#include "config.h"
#include "queues.h"
#include "kff_random_access.h"
//************************************************************************************************************
// CFastqFilter - filter of reads
//************************************************************************************************************
class CFastqFilter
{
private:
CFilteringParams::FilterMode mode;
CPartQueue *input_part_queue, *filtered_part_queue;
CMemoryPool *pmm_fastq_reader;
CMemoryPool *pmm_fastq_filter;
CFilteringParams::file_type input_file_type, output_file_type;
CKffAndKMCRandomAccess& kmc_api;
uint64 output_part_size;
uchar* input_part;
uint64 input_part_size;
uint64 input_part_pos;
uchar* output_part;
uint64 output_part_pos;
std::vector<uint32> counters;
std::string read;
struct {
uint64 read_header_start;
uint64 read_header_end;
uint64 read_start;
uint64 read_end;
uint64 quality_header_start;
uint64 quality_header_end;
uint64 quality_start;
uint64 quality_end;
uint64 end;
}seq_desc;
uint32 trim_len; //for trim mode
bool use_float_value;
float f_max_kmers;
float f_min_kmers;
uint32 n_max_kmers;
uint32 n_min_kmers;
uint32 kmer_len;
template<class Helper> void ProcessImpl();
bool NextSeqFastq();
bool NextSeqFasta();
bool FilterRead();
bool FilterReadTrim();
void HardMask();
public:
CFastqFilter(CFilteringParams& Params, CFilteringQueues& Queues, CKffAndKMCRandomAccess& kmc_api);
void Process();
private: //Helpers classes for ProcessImpl
class FastqToFastqHelper;
class FastqToFastaHelper;
class FastaToFastaHelper;
class TrimFastqToFastqHelper;
class TrimFastqToFastaHelper;
class TrimFastaToFastaHelper;
class HardMaskFastqToFastqHelper;
class HardMaskFastqToFastaHelper;
class HardMaskFastaToFastaHelper;
};
//************************************************************************************************************
// CWFastqFilter - wrapper for CFastqFilter class - for multithreading purposes
//************************************************************************************************************
class CWFastqFilter
{
std::unique_ptr<CFastqFilter> ff;
public:
CWFastqFilter(CFilteringParams& Params, CFilteringQueues& Queues, CKffAndKMCRandomAccess& kmc_api);
void operator()();
};
#endif
// ***** EOF
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