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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
*/
#include "kmer_file_header.h"
#include "kff_info_reader.h"
#include <cstring>
#include <set>
/*****************************************************************************************************************************/
/******************************************************** CONSTRUCTOR ********************************************************/
/*****************************************************************************************************************************/
CKmerFileHeader::CKmerFileHeader(std::string file_name)
{
if (is_kff_file(file_name))
{
kmer_file_type = KmerFileType::KFF1;
read_from_kff_file(file_name);
return;
}
file_name += ".kmc_pre";
FILE* file = my_fopen(file_name.c_str(), "rb");
if (!file)
{
std::cerr << "Error: Cannot open file " << file_name << "\n";
exit(1);
}
char marker[4];
if (fread(marker, 1, 4, file) != 4)
{
std::cerr << "Error while reading start marker in " << file_name << "\n";
exit(1);
}
if (strncmp(marker, "KMCP", 4) != 0)
{
std::cerr << "Error: wrong start marker in " << file_name << "\n";
exit(1);
}
my_fseek(file, -4, SEEK_END);
if (fread(marker, 1, 4, file) != 4)
{
std::cerr << "Error while reading end marker in " << file_name << "\n";
exit(1);
}
if (strncmp(marker, "KMCP", 4) != 0)
{
std::cerr << "Error: wrong end marker in " << file_name << "\n";
exit(1);
}
my_fseek(file, 0, SEEK_END);
uint64 file_size = my_ftell(file);
my_fseek(file, -8, SEEK_END);
load_uint(file, header_offset);
my_fseek(file, -12, SEEK_END);
load_uint(file, db_version);
kmer_file_type = db_version == 0x200 ? KmerFileType::KMC2 : KmerFileType::KMC1;
my_fseek(file, 0LL - (header_offset + 8), SEEK_END);
load_uint(file, kmer_len);
load_uint(file, mode);
load_uint(file, counter_size);
load_uint(file, lut_prefix_len);
if (kmer_file_type == KmerFileType::KMC2)
load_uint(file, signature_len);
load_uint(file, min_count);
uint32_t max_count_lo;
load_uint(file, max_count_lo);
load_uint(file, total_kmers);
uchar both_s_tmp;
load_uint(file, both_s_tmp);
both_strands = both_s_tmp == 1;
both_strands = !both_strands;
fseek(file, 3, SEEK_CUR);
uint32_t max_count_hi;
load_uint(file, max_count_hi);
max_count = (((uint64_t)max_count_hi) << 32) + max_count_lo;
fclose(file);
if (kmer_file_type == KmerFileType::KMC2)
{
uint32 single_lut_size = (1ull << (2 * lut_prefix_len)) * sizeof(uint64);
uint32 map_size = ((1 << 2 * signature_len) + 1) * sizeof(uint32);
no_of_bins = (uint32)((file_size - sizeof(uint64) - 12 - header_offset - map_size) / single_lut_size);
}
}
bool CKmerFileHeader::is_kff_file(std::string& fname)
{
auto file = my_fopen(fname.c_str(), "rb");
if (!file)
{
file = my_fopen((fname + ".kff").c_str(), "rb");
if (file)
fname += ".kff";
else
return false;
}
char marker_start[3];
fread(marker_start, 1, 3, file);
char marker_end[3];
my_fseek(file, -3, SEEK_END);
fread(marker_end, 1, 3, file);
if (strncmp("KFF", marker_start, 3) || strncmp("KFF", marker_end, 3))
return false;
return true;
}
void CKmerFileHeader::read_from_kff_file(const std::string& fname)
{
CKFFInfoReader kff_reader(fname);
kff_file_struct = kff_reader.GetKffFileStruct();
std::set<uint64_t> k_values;
this->counter_size = 0;
if (kff_file_struct.scopes.empty())
{
std::cerr << "Error: no not-empty scope was found in KFF file. Make sure KFF file is fully indexed\n";
exit(1);
}
for (auto& s : kff_file_struct.scopes)
{
k_values.insert(s.kmer_size);
if (!s.ordered)
{
std::cerr << "Error: kmc_tools requires all KFF sections to be ordered\n";
exit(1);
}
for (auto& section: s.data_sections)
if (!(section.type == KFFDataSectionType::RAW))
{
std::cerr << "Error: currently kmc_tools supports only raw KFF sections\n";
exit(1);
}
if (s.data_size > this->counter_size)
this->counter_size = s.data_size;
}
this->min_count = GetFromFooterOrDefault("min_count", 1);
this->max_count = GetFromFooterOrDefault("max_count", std::numeric_limits<uint32>::max());
this->both_strands = kff_file_struct.both_strands;
if (k_values.size() == 1)
kmer_len = *k_values.begin();
else
{
std::cerr << "Error: only KFF files with single k value are supported. This file contains following k values:";
for (auto k : k_values)
std::cerr << " " << k;
std::cerr << "\n";
exit(1);
}
}
// ***** EOF
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