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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: 3.2.4
Date : 2024-02-09
*/
#ifndef _SPLITTER_H
#define _SPLITTER_H
#include "defs.h"
#include "kmer.h"
#include "kb_collector.h"
#include "queues.h"
#include "s_mapper.h"
#include "../kmc_api/mmer.h"
#include <stdio.h>
#include <vector>
#include "small_k_buf.h"
#include "bam_utils.h"
using namespace std;
//************************************************************************************************************
// CSplitter class - splits kmers into bins according to their signatures
//************************************************************************************************************
class CSplitter
{
uint64 total_kmers = 0;
uchar *part;
uint64_t part_size, part_pos;
std::vector<std::unique_ptr<CKmerBinCollector>> bins;
CBinPartQueue *bin_part_queue;
CMemoryPool *pmm_reads;
int64 mem_part_pmm_bins;
int64 mem_part_pmm_reads;
char codes[256];
InputType file_type;
bool both_strands;
uint32_t curr_read_len = 0;
uint32 kmer_len;
//uint32 prefix_len;
uint32 signature_len;
uint32 n_bins;
uint64 n_reads;//for multifasta its a sequences counter
CSignatureMapper* s_mapper;
bool homopolymer_compressed;
CntHashEstimator* ntHashEstimator;
bool GetSeqLongRead(char *seq, uint32 &seq_size, uchar header_marker);
bool GetSeq(char *seq, uint32 &seq_size, ReadType read_type);
void HomopolymerCompressSeq(char* seq, uint32 &seq_size);
public:
static uint32 MAX_LINE_SIZE;
CSplitter(CKMCParams &Params, CKMCQueues &Queues);
void InitBins(CKMCParams &Params, CKMCQueues &Queues);
void CalcStats(uchar* _part, uint64 _part_size, ReadType read_type, uint32* _stats);
bool ProcessReadsOnlyEstimate(uchar* _part, uint64 _part_size, ReadType read_type);
bool ProcessReads(uchar *_part, uint64 _part_size, ReadType read_type);
template<typename COUNTER_TYPE> bool ProcessReadsSmallK(uchar *_part, uint64 _part_size, ReadType read_type, CSmallKBuf<COUNTER_TYPE>& small_k_buf);
void Complete();
inline void GetTotal(uint64 &_n_reads);
inline uint64 GetTotalKmers();
};
//----------------------------------------------------------------------------------
// Return the number of reads processed by splitter
void CSplitter::GetTotal(uint64 &_n_reads)
{
_n_reads = n_reads;
}
//----------------------------------------------------------------------------------
// Return the number of kmers processed by splitter (!!! only for small k optimization)
uint64 CSplitter::GetTotalKmers()
{
return total_kmers;
}
//************************************************************************************************************
// CWSplitter class - wrapper for multithreading purposes
//************************************************************************************************************
//----------------------------------------------------------------------------------
class CWSplitter {
CPartQueue *pq;
CBinPartQueue *bpq;
CMemoryPool *pmm_fastq;
std::unique_ptr<CSplitter> spl;
uint64 n_reads;
public:
CWSplitter(CKMCParams &Params, CKMCQueues &Queues);
void operator()();
void GetTotal(uint64 &_n_reads);
~CWSplitter();
};
//************************************************************************************************************
// CWStatsSplitter class - wrapper for multithreading purposes
//************************************************************************************************************
//----------------------------------------------------------------------------------
class CWStatsSplitter {
CStatsPartQueue *spq;
CMemoryPool *pmm_fastq, *pmm_stats;
uint32 *stats;
std::unique_ptr<CSplitter> spl;
uint32 signature_len;
KMC::IProgressObserver* progressObserver;
public:
CWStatsSplitter(CKMCParams &Params, CKMCQueues &Queues);
~CWStatsSplitter();
void operator()();
void GetStats(uint32* _stats);
};
//************************************************************************************************************
// CWSmallKSplitter class - wrapper for multithreading purposes
//************************************************************************************************************
//----------------------------------------------------------------------------------
template <typename COUNTER_TYPE> class CWSmallKSplitter {
CPartQueue *pq;
CMemoryPool *pmm_fastq, *pmm_small_k;
CSmallKBuf<COUNTER_TYPE> small_k_buf;
std::unique_ptr<CSplitter> spl;
uint64 n_reads;
uint64 total_kmers;
uint32 kmer_len;
public:
CWSmallKSplitter(CKMCParams &Params, CKMCQueues &Queues);
~CWSmallKSplitter();
void operator()();
void GetTotal(uint64 &_n_reads);
CSmallKBuf<COUNTER_TYPE> GetResult()
{
return small_k_buf;
}
uint64 GetTotalKmers()
{
if (spl)
return spl->GetTotalKmers();
return total_kmers;
}
void Release()
{
pmm_small_k->free(small_k_buf.buf);
}
};
//************************************************************************************************************
// CWEstimateOnlySplitter class - wrapper for multithreading purposes
//************************************************************************************************************
//----------------------------------------------------------------------------------
class CWEstimateOnlySplitter {
CPartQueue* pq;
CBinPartQueue* bpq;
CMemoryPool* pmm_fastq;
std::unique_ptr<CSplitter> spl;
uint64 n_reads;
public:
CWEstimateOnlySplitter(CKMCParams& Params, CKMCQueues& Queues);
void operator()();
void GetTotal(uint64& _n_reads);
~CWEstimateOnlySplitter();
};
#endif
// ***** EOF
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