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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 _KB_COLLECTOR_H
#define _KB_COLLECTOR_H
#include "defs.h"
#include "params.h"
#include "kmer.h"
#include "queues.h"
#include "radix.h"
#include "rev_byte.h"
#include <string>
#include <algorithm>
#include <numeric>
#include <array>
#include <vector>
#include <stdio.h>
using namespace std;
//----------------------------------------------------------------------------------
// Class collecting kmers belonging to a single bin
class CKmerBinCollector
{
list<pair<uint64, uint64>> expander_parts; //range, n_plus_x_recs_in_range
uint64 prev_n_plus_x_recs = 0;
uint64 prev_pos = 0;
enum comparision_state { kmer_smaller, rev_smaller, equals };
uint32 bin_no;
CBinPartQueue *bin_part_queue;
CBinDesc *bd;
uint32 kmer_len;
uchar* buffer;
uint32 buffer_size;
uint32 buffer_pos;
uint32 super_kmer_no = 0;
const uint32 max_super_kmers_expander_pack = 1ul << 12;
CMemoryPool *pmm_bins;
uint32 n_recs;
uint32 n_plus_x_recs;
uint32 n_super_kmers;
uint32 max_x;
uint32 kmer_bytes;
bool both_strands;
template<unsigned DIVIDE_FACTOR> void update_n_plus_x_recs(char* seq, uint32 n);
public:
CKmerBinCollector(CKMCQueues& Queues, CKMCParams& Params, uint32 _buffer_size, uint32 _bin_no);
void PutExtendedKmer(char* seq, uint32 n);
void Flush();
};
//---------------------------------------------------------------------------------
template<unsigned DIVIDE_FACTOR> void CKmerBinCollector::update_n_plus_x_recs(char* seq, uint32 n)
{
uchar kmer, rev;
uint32 kmer_pos = 4;
uint32 rev_pos = kmer_len;
uint32 x;
kmer = (seq[0] << 6) + (seq[1] << 4) + (seq[2] << 2) + seq[3];
rev = ((3 - seq[kmer_len - 1]) << 6) + ((3 - seq[kmer_len - 2]) << 4) + ((3 - seq[kmer_len - 3]) << 2) + (3 - seq[kmer_len - 4]);
x = 0;
comparision_state current_state, new_state;
if (kmer < rev)
current_state = kmer_smaller;
else if (rev < kmer)
current_state = rev_smaller;
else
current_state = equals;
for (uint32 i = 0; i < n - kmer_len; ++i)
{
rev >>= 2;
rev += (3 - seq[rev_pos++]) << 6;
kmer <<= 2;
kmer += seq[kmer_pos++];
if (kmer < rev)
new_state = kmer_smaller;
else if (rev < kmer)
new_state = rev_smaller;
else
new_state = equals;
if (new_state == current_state)
{
if (current_state == equals)
++n_plus_x_recs;
else
++x;
}
else
{
current_state = new_state;
n_plus_x_recs += 1 + x / DIVIDE_FACTOR;
x = 0;
}
}
n_plus_x_recs += 1 + x / DIVIDE_FACTOR;
}
#endif
// ***** EOF
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