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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: 2.3.0
Date : 2015-08-21
*/
#ifndef _DUMP_WRITER_H
#define _DUMP_WRITER_H
#include "defs.h"
#include "kmer.h"
#include "nc_utils.h"
#include "config.h"
#include <fstream>
//wrapper to simplify interface
//For kmc1 input and kmc2 input without -s parameter
template<typename KMCDB, unsigned SIZE, bool SORTED>
class CKMCDBForDump
{
KMCDB kmcdb;
public:
CKMCDBForDump() :
kmcdb(CConfig::GetInstance().headers.front(), CConfig::GetInstance().input_desc.front(), CConfig::GetInstance().percent_progress, KMCDBOpenMode::sequential){}
bool NextKmer(CKmer<SIZE>& kmer, uint32& counter)
{
return kmcdb.NextKmerSequential(kmer, counter);
}
};
//specialization for -s parameter nad kmc2 input
template<unsigned SIZE>
class CKMCDBForDump<CKMC2DbReader<SIZE>, SIZE, true>
{
CKMC2DbReader<SIZE>* kmcdb;
CBundle<SIZE> bundle;
public:
CKMCDBForDump() :
kmcdb(new CKMC2DbReader<SIZE>(CConfig::GetInstance().headers.front(), CConfig::GetInstance().input_desc.front(), CConfig::GetInstance().percent_progress, KMCDBOpenMode::sorted)),
bundle(kmcdb){}
bool NextKmer(CKmer<SIZE>& kmer, uint32& counter)
{
if(!bundle.Finished())
{
kmer = bundle.TopKmer();
counter = bundle.TopCounter();
bundle.Pop();
return true;
}
return false;
}
};
template<typename KMCDB, unsigned SIZE>
class CDumpWriter
{
static const uint32 OVERHEAD_SIZE = 1000;
KMCDB& kmcdb;
COutputDesc output_desc;
uint32 kmer_len;
uint32 kmer_bytes;
CConfig& config;
uint32 in_first_byte;
char* buf;
uint32 buf_size;
uint32 buf_pos;
struct DumpOpt
{
char* opt_ACGT;
DumpOpt()
{
opt_ACGT = new char[1024];
char codes[] = { 'A', 'C', 'G', 'T' };
uint32 pos = 0;
for (uint32 kmer = 0; kmer < 256; ++kmer)
{
opt_ACGT[pos++] = codes[(kmer >> 6) & 3];
opt_ACGT[pos++] = codes[(kmer >> 4) & 3];
opt_ACGT[pos++] = codes[(kmer >> 2) & 3];
opt_ACGT[pos++] = codes[kmer & 3];
}
}
~DumpOpt()
{
delete[]opt_ACGT;
}
}opt;
void kmerToStr(CKmer<SIZE>& kmer, char* kmer_str)
{
//first byte
char* base = opt.opt_ACGT + 4 * kmer.get_byte(kmer_bytes - 1) + 4 - in_first_byte;
for(uint32 i = 0 ; i < in_first_byte ; ++i)
*kmer_str++ = *base++;
//rest
for (int pos = kmer_bytes - 2; pos >= 0; --pos)
{
base = opt.opt_ACGT + 4 * kmer.get_byte(pos);
*kmer_str++ = *base++;
*kmer_str++ = *base++;
*kmer_str++ = *base++;
*kmer_str++ = *base++;
}
}
public:
CDumpWriter(KMCDB& kmcdb) :kmcdb(kmcdb), output_desc(CConfig::GetInstance().output_desc), config(CConfig::GetInstance())
{
kmer_len = config.headers.front().kmer_len;
kmer_bytes = (kmer_len + 3) / 4;
in_first_byte = kmer_len % 4;
if (in_first_byte == 0)
in_first_byte = 4;
}
bool Process()
{
CKmer<SIZE> kmer;
uint32 counter;
uint32 counter_len;
FILE* file = fopen(output_desc.file_src.c_str(), "wb");
if (!file)
{
std::cout << "Error: cannot open file: " << output_desc.file_src << "\n";
exit(1);
}
buf_pos = 0;
buf_size = DUMP_BUF_SIZE;
buf = new char[buf_size];
//while (kmcdb.NextKmerSequential(kmer, counter))
while (kmcdb.NextKmer(kmer, counter))
{
if (counter >= output_desc.cutoff_min && counter <= output_desc.cutoff_max)
{
kmerToStr(kmer, buf + buf_pos);
buf[buf_pos + kmer_len] = '\t';
counter_len = CNumericConversions::Int2PChar(counter, (uchar*)(buf + buf_pos + kmer_len + 1));
buf[buf_pos + kmer_len + 1 + counter_len] = '\n';
buf_pos += kmer_len + 2 + counter_len;
if (buf_pos + OVERHEAD_SIZE > buf_size)
{
fwrite(buf, 1, buf_pos, file);
buf_pos = 0;
}
}
}
//save rest if necessary
if (buf_pos)
{
fwrite(buf, 1, buf_pos, file);
buf_pos = 0;
}
fclose(file);
delete[] buf;
return true;
}
};
#endif
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