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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
*/
#include "kb_collector.h"
CKmerBinCollector::CKmerBinCollector(CKMCQueues& Queues, CKMCParams& Params, uint32 _buffer_size, uint32 _bin_no)
{
bin_part_queue = Queues.bpq.get();
kmer_len = Params.kmer_len;
bd = Queues.bd.get();
buffer_size = _buffer_size;
pmm_bins = Queues.pmm_bins.get();
max_x = Params.max_x;
bin_no = _bin_no;
n_recs = 0;
n_super_kmers = 0;
n_plus_x_recs = 0;
buffer_pos = 0;
pmm_bins->reserve(buffer);
both_strands = Params.both_strands;
kmer_bytes = (kmer_len + 3) / 4;
}
//---------------------------------------------------------------------------------
void CKmerBinCollector::PutExtendedKmer(char* seq, uint32 n)
{
if (super_kmer_no >= max_super_kmers_expander_pack)
{
expander_parts.push_back(make_pair(buffer_pos - prev_pos, n_plus_x_recs - prev_n_plus_x_recs));
prev_pos = buffer_pos;
prev_n_plus_x_recs = n_plus_x_recs;
super_kmer_no = 0;
}
uint32 bytes = 1 + (n + 3) / 4;
if (buffer_pos + bytes > buffer_size)
{
//send current buff
Flush();
pmm_bins->reserve(buffer);
buffer_pos = 0;
n_recs = 0;
n_super_kmers = 0;
n_plus_x_recs = 0;
}
buffer[buffer_pos++] = n - kmer_len;
for (uint32 i = 0, j = 0; i < n / 4; ++i, j += 4)
buffer[buffer_pos++] = (seq[j] << 6) + (seq[j + 1] << 4) + (seq[j + 2] << 2) + seq[j + 3];
switch (n % 4)
{
case 1:
buffer[buffer_pos++] = (seq[n - 1] << 6);
break;
case 2:
buffer[buffer_pos++] = (seq[n - 2] << 6) + (seq[n - 1] << 4);
break;
case 3:
buffer[buffer_pos++] = (seq[n - 3] << 6) + (seq[n - 2] << 4) + (seq[n - 1] << 2);
break;
}
++n_super_kmers;
n_recs += n - kmer_len + 1;
if (max_x) ///for max_x = 0 k-mers (not k+x-mers) will be sorted
{
if (!both_strands)
n_plus_x_recs += 1 + (n - kmer_len) / (max_x + 1);
else
{
switch (max_x)
{
case 1: update_n_plus_x_recs<2>(seq, n); break;
case 2: update_n_plus_x_recs<3>(seq, n); break;
case 3: update_n_plus_x_recs<4>(seq, n); break;
}
}
}
}
//---------------------------------------------------------------------------------
void CKmerBinCollector::Flush()
{
if (prev_pos < buffer_pos)
{
expander_parts.push_back(make_pair(buffer_pos - prev_pos, n_plus_x_recs - prev_n_plus_x_recs));
}
prev_pos = 0;
prev_n_plus_x_recs = 0;
super_kmer_no = 0;
bin_part_queue->push(bin_no, buffer, buffer_pos, buffer_size, expander_parts);
expander_parts.clear();
bd->update(bin_no, buffer_pos, n_recs, n_plus_x_recs, n_super_kmers);
}
// ***** EOF
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