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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 _BKB_SUBBIN_H
#define _BKB_SUBBIN_H
//************************************************************************************************************
// CSubBin - sorted k-mers (part of some bin), used in strict memory mode
//************************************************************************************************************
template<unsigned SIZE>
class CSubBin
{
CDiskLogger* disk_logger;
uchar* raw_lut;
uint64* lut;
uint32 current_prefix;
uchar* suff_buff;
uint64 suff_buff_size, max_in_suff_buff, lut_start_pos_in_file;
uint64 left_to_read, n_kmers, in_current_prefix;
uint32 kmer_len, lut_size, lut_buff_recs, lut_offset, cur_in_suff_buff, suff_buff_pos;
string name;
FILE* file;
uint32 suff_rec_len, lut_prefix_len, counter_size, suffix_bytes;
uint64 size;
void read_next_lut_part();
public:
bool get_min(CKmer<SIZE>& kmer, uint32& count);
CSubBin(CDiskLogger* _disk_logger)
{
lut_size = 0;
disk_logger = _disk_logger;
}
void init(FILE* _file, uint64 _size, uint32 _lut_prefix_len, uint64 _n_kmers, string _name, uint32 _kmer_len, uchar* _lut_buff, uint32 _lut_buff_size, uchar* _suff_buff, uint64 _suff_buff_size);
};
//--------------------------------------------------------------------------
template<unsigned SIZE>
void CSubBin<SIZE>::read_next_lut_part()
{
uint32 to_read = MIN(lut_size - lut_offset, lut_buff_recs);
lut_offset += lut_buff_recs;
if (to_read)
{
uint64 prev_pos = my_ftell(file);
my_fseek(file, lut_start_pos_in_file + (lut_offset - lut_buff_recs) * sizeof(uint64), SEEK_SET);
if (fread(lut, sizeof(uint64), to_read, file) != to_read)
{
std::ostringstream ostr;
ostr << "Error while reading file : " << name;
CCriticalErrorHandler::Inst().HandleCriticalError(ostr.str());
}
my_fseek(file, prev_pos, SEEK_SET);
}
}
//--------------------------------------------------------------------------
template<unsigned SIZE>
bool CSubBin<SIZE>::get_min(CKmer<SIZE>& kmer, uint32& count)
{
while (true)
{
if (current_prefix >= lut_offset)
{
read_next_lut_part();
}
if (in_current_prefix >= lut[current_prefix + lut_buff_recs - lut_offset])
{
++current_prefix;
in_current_prefix = 0;
}
else
{
++in_current_prefix;
break;
}
if (current_prefix >= lut_size)
{
fclose(file);
remove(name.c_str());
disk_logger->log_remove(size);
return false;
}
}
uchar *suf_rec = suff_buff + suff_buff_pos * suff_rec_len;
uint32 tmp = current_prefix;
uint32 pos = suffix_bytes;
kmer.load(suf_rec, suffix_bytes);
while (tmp)
{
kmer.set_byte(pos++, (uchar)tmp & 0xFF);
tmp >>= 8;
}
count = 0;
for (uint32 i = 0; i < counter_size; ++i)
count += (*suf_rec++) << (8 * i);
suff_buff_pos++;
if (suff_buff_pos >= cur_in_suff_buff)
{
cur_in_suff_buff = (uint32)fread(suff_buff, 1, MIN(suff_rec_len * max_in_suff_buff, left_to_read), file) / suff_rec_len;
suff_buff_pos = 0;
left_to_read -= cur_in_suff_buff * suff_rec_len;
}
return true;
}
//--------------------------------------------------------------------------
template<unsigned SIZE>
void CSubBin<SIZE>::init(FILE* _file, uint64 _size, uint32 _lut_prefix_len, uint64 _n_kmers, string _name, uint32 _kmer_len, uchar* _lut_buff, uint32 _lut_buff_size, uchar* _suff_buff, uint64 _suff_buff_size)
{
size = _size;
lut = (uint64*)_lut_buff;
lut_buff_recs = _lut_buff_size / sizeof(uint64);
suff_buff = _suff_buff;
suff_buff_size = _suff_buff_size;
lut_offset = 0;
lut_prefix_len = _lut_prefix_len;
kmer_len = _kmer_len;
suffix_bytes = (kmer_len - lut_prefix_len) / 4;
file = _file;
n_kmers = _n_kmers;
name = _name;
counter_size = sizeof(uint32);
lut_size = (1 << lut_prefix_len * 2);
suff_rec_len = (kmer_len - lut_prefix_len) / 4 + counter_size;
left_to_read = suff_rec_len * n_kmers;
max_in_suff_buff = suff_buff_size / suff_rec_len;
lut_start_pos_in_file = n_kmers * suff_rec_len;
rewind(file);
read_next_lut_part();
cur_in_suff_buff = (uint32)fread(suff_buff, 1, MIN(max_in_suff_buff * suff_rec_len, left_to_read), file) / suff_rec_len;
left_to_read -= cur_in_suff_buff * suff_rec_len;
current_prefix = 0;
in_current_prefix = 0;
suff_buff_pos = 0;
}
#endif
// ***** EOF
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