/usr/include/kmc/kmer_api.h is in libkmc-dev 2.3+dfsg-5.
This file is owned by root:root, with mode 0o644.
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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 and Agnieszka Debudaj-Grabysz
Version: 2.3.0
Date : 2015-08-21
*/
#ifndef _KMER_API_H
#define _KMER_API_H
#include "kmer_defs.h"
#include <string>
#include <iostream>
#include <vector>
#include "mmer.h"
class CKMCFile;
class CKmerAPI
{
protected:
uint64 *kmer_data; // An array to store kmer's data. On 64 bits 32 symbols can be stored
// Data are shifted to let sufix's symbols to start with a border of a byte
uint32 kmer_length; // Kmer's length, in symbols
uchar byte_alignment; // A number of "empty" symbols placed before prefix to let sufix's symbols to start with a border of a byte
uint32 no_of_rows; // A number of 64-bits words allocated for kmer_data
friend class CKMCFile;
//----------------------------------------------------------------------------------
inline void clear()
{
memset(kmer_data, 0, sizeof(*kmer_data) * no_of_rows);
}
//----------------------------------------------------------------------------------
inline void insert2bits(uint32 pos, uchar val)
{
kmer_data[(pos + byte_alignment) >> 5] += (uint64)val << (62 - (((pos + byte_alignment) & 31) * 2));
}
inline uchar extract2bits(uint32 pos)
{
return (kmer_data[(pos + byte_alignment) >> 5] >> (62 - (((pos + byte_alignment) & 31) * 2))) & 3;
}
//----------------------------------------------------------------------------------
inline void SHL_insert2bits(uchar val)
{
kmer_data[0] <<= 2;
if (byte_alignment)
{
uint64 mask = ~(((1ull << 2 * byte_alignment) - 1) << (64 - 2 * byte_alignment));
kmer_data[0] &= mask;
}
for (uint32 i = 1; i < no_of_rows; ++i)
{
kmer_data[i - 1] += kmer_data[i] >> 62;
kmer_data[i] <<= 2;
}
kmer_data[no_of_rows - 1] += (uint64)val << (62 - (((kmer_length - 1 + byte_alignment) & 31) * 2));
}
//----------------------------------------------------------------------------------
inline void SHR_insert2bits(uchar val)
{
for (uint32 i = no_of_rows - 1; i > 0; --i)
{
kmer_data[i] >>= 2;
kmer_data[i] += kmer_data[i - 1] << 62;
}
kmer_data[0] >>= 2;
kmer_data[no_of_rows - 1] &= ~((1ull << ((32 - (kmer_length + byte_alignment - (no_of_rows - 1) * 32)) * 2)) - 1);//mask falling of symbol
kmer_data[0] += ((uint64)val << 62) >> (byte_alignment * 2);
}
// ----------------------------------------------------------------------------------
inline void from_binary(const char* kmer)
{
clear();
for (uint32 i = 0; i < kmer_length; ++i)
insert2bits(i, kmer[i]);
}
// ----------------------------------------------------------------------------------
inline void from_binary_rev(const char* kmer)
{
clear();
for (uint32 i = 0; i < kmer_length; ++i)
insert2bits(i, 3 - kmer[kmer_length - i - 1]);
}
// ----------------------------------------------------------------------------------
template<typename RandomAccessIterator>
inline void to_string_impl(RandomAccessIterator iter)
{
uchar *byte_ptr;
uchar c;
uchar temp_byte_alignment = byte_alignment;
uint32 cur_string_size = 0;
for (uint32 row_counter = 0; row_counter < no_of_rows; row_counter++)
{
byte_ptr = reinterpret_cast<uchar*>(&kmer_data[row_counter]);
byte_ptr += 7; // shift a pointer towards a MSB
for (uint32 i = 0; (i < kmer_length) && (i < 32); i += 4) // 32 symbols of any "row" in kmer_data
{
if ((i == 0) && temp_byte_alignment) // check if a byte_alignment placed before a prefix is to be skipped
temp_byte_alignment--;
else
{
c = 0xc0 & *byte_ptr; //11000000
c = c >> 6;
*(iter + cur_string_size++) = char_codes[c];
if (cur_string_size == kmer_length) break;
}
if ((i == 0) && temp_byte_alignment) // check if a byte_alignment placed before a prefix is to be skipped
temp_byte_alignment--;
else
{
c = 0x30 & *byte_ptr; //00110000
c = c >> 4;
*(iter + cur_string_size++) = char_codes[c];
if (cur_string_size == kmer_length) break;
}
if ((i == 0) && temp_byte_alignment) // check if a byte_alignment placed before a prefix is to be skipped
temp_byte_alignment--;
else
{
c = 0x0c & *byte_ptr; //00001100
c = c >> 2;
*(iter + cur_string_size++) = char_codes[c];
if (cur_string_size == kmer_length) break;
}
// no need to check byte alignment as its length is at most 3
c = 0x03 & *byte_ptr; //00000011
*(iter + cur_string_size++) = char_codes[c];
if (cur_string_size == kmer_length) break;
byte_ptr--;
}
}
}
// ----------------------------------------------------------------------------------
template<typename RandomAccessIterator>
inline bool from_string_impl(const RandomAccessIterator iter, uint32 len)
{
unsigned char c_char;
uchar c_binary;
uchar temp_byte_alignment;
if (kmer_length != len)
{
if (kmer_length && kmer_data)
delete[] kmer_data;
kmer_length = len;
if (kmer_length % 4)
byte_alignment = 4 - (kmer_length % 4);
else
byte_alignment = 0;
if (kmer_length != 0)
{
no_of_rows = (((kmer_length + byte_alignment) % 32) ? (kmer_length + byte_alignment) / 32 + 1 : (kmer_length + byte_alignment) / 32);
//no_of_rows = (int)ceil((double)(kmer_length + byte_alignment) / 32);
kmer_data = new uint64[no_of_rows];
//memset(kmer_data, 0, sizeof(*kmer_data) * no_of_rows);
}
}
memset(kmer_data, 0, sizeof(*kmer_data) * no_of_rows);
temp_byte_alignment = byte_alignment;
uint32 i = 0;
uint32 i_in_string = 0;
uchar *byte_ptr;
for (uint32 row_index = 0; row_index < no_of_rows; row_index++)
{
byte_ptr = reinterpret_cast<uchar*>(&kmer_data[row_index]);
byte_ptr += 7; // shift a pointer towards a MSB
while (i < kmer_length)
{
if ((i_in_string == 0) && temp_byte_alignment) // check if a byte_alignment placed before a prefix is to be skipped
{
temp_byte_alignment--;
i++;
}
else
{
c_char = *(iter + i_in_string);
c_binary = num_codes[c_char];
c_binary = c_binary << 6; //11000000
*byte_ptr = *byte_ptr | c_binary;
i++;
i_in_string++;
if (i_in_string == kmer_length) break;
}
if ((i_in_string == 0) && temp_byte_alignment) // check if a byte_alignment placed before a prefix is to be skipped
{
temp_byte_alignment--;
i++;
}
else
{
c_char = *(iter + i_in_string);
c_binary = num_codes[c_char];
c_binary = c_binary << 4;
*byte_ptr = *byte_ptr | c_binary;
i++;
i_in_string++;
if (i_in_string == kmer_length) break;
}
//!!!if((i == 0) && temp_byte_alignment) //poprawka zg3oszona przez Maaka D3ugosza // check if a byte_alignment placed before a prefix is to be skipped
if ((i_in_string == 0) && temp_byte_alignment) // check if a byte_alignment placed before a prefix is to be skipped
{
temp_byte_alignment--;
i++;
}
else
{
c_char = *(iter + i_in_string);
c_binary = num_codes[c_char];
c_binary = c_binary << 2;
*byte_ptr = *byte_ptr | c_binary;
i++;
i_in_string++;
if (i_in_string == kmer_length) break;
}
c_char = *(iter + i_in_string);
c_binary = num_codes[c_char];
*byte_ptr = *byte_ptr | c_binary;
i++;
i_in_string++;
if (i_in_string == kmer_length) break;
if (i % 32 == 0)
break; //check if a new "row" is to be started
byte_ptr--;
}
};
return true;
}
public:
static const char char_codes[];
static char num_codes[256];
static uchar rev_comp_bytes_LUT[];
static uint64 alignment_mask[];
struct _si
{
_si()
{
for (int i = 0; i < 256; i++)
num_codes[i] = -1;
num_codes['A'] = num_codes['a'] = 0;
num_codes['C'] = num_codes['c'] = 1;
num_codes['G'] = num_codes['g'] = 2;
num_codes['T'] = num_codes['t'] = 3;
}
} static _init;
// ----------------------------------------------------------------------------------
// The constructor creates kmer for the number of symbols equal to length.
// The array kmer_data has the size of ceil((length + byte_alignment) / 32))
// IN : length - a number of symbols of a kmer
// ----------------------------------------------------------------------------------
inline CKmerAPI(uint32 length = 0)
{
if(length)
{
if(length % 4)
byte_alignment = 4 - (length % 4);
else
byte_alignment = 0;
no_of_rows = (((length + byte_alignment) % 32) ? (length + byte_alignment) / 32 + 1 : (length + byte_alignment) / 32);
//no_of_rows = (int)ceil((double)(length + byte_alignment) / 32);
kmer_data = new uint64[no_of_rows];
memset(kmer_data, 0, sizeof(*kmer_data) * no_of_rows);
}
else
{
kmer_data = NULL;
no_of_rows = 0;
byte_alignment = 0;
}
kmer_length = length;
};
//-----------------------------------------------------------------------
// The destructor
//-----------------------------------------------------------------------
inline ~CKmerAPI()
{
if (kmer_data != NULL)
delete [] kmer_data;
};
//-----------------------------------------------------------------------
// The copy constructor
//-----------------------------------------------------------------------
inline CKmerAPI(const CKmerAPI &kmer)
{
kmer_length = kmer.kmer_length;
byte_alignment = kmer.byte_alignment;
no_of_rows = kmer.no_of_rows;
kmer_data = new uint64[no_of_rows];
for(uint32 i = 0; i < no_of_rows; i++)
kmer_data[i] = kmer.kmer_data[i];
};
//-----------------------------------------------------------------------
// The operator =
//-----------------------------------------------------------------------
inline CKmerAPI& operator=(const CKmerAPI &kmer)
{
if(kmer.kmer_length != kmer_length)
{
if(kmer_length && kmer_data)
delete [] kmer_data;
kmer_length = kmer.kmer_length;
byte_alignment = kmer.byte_alignment;
no_of_rows = kmer.no_of_rows;
kmer_data = new uint64[no_of_rows];
}
for(uint32 i = 0; i < no_of_rows; i++)
kmer_data[i] = kmer.kmer_data[i];
return *this;
};
//-----------------------------------------------------------------------
// The operator ==
//-----------------------------------------------------------------------
inline bool operator==(const CKmerAPI &kmer)
{
if(kmer.kmer_length != kmer_length)
return false;
for(uint32 i = 0; i < no_of_rows; i++)
if(kmer.kmer_data[i] != kmer_data[i])
return false;
return true;
};
//-----------------------------------------------------------------------
// Operator < . If arguments differ in length a result is undefined
//-----------------------------------------------------------------------
inline bool operator<(const CKmerAPI &kmer)
{
if(kmer.kmer_length != kmer_length)
return false;
for(uint32 i = 0; i < no_of_rows; i++)
if(kmer.kmer_data[i] > kmer_data[i])
return true;
else
if(kmer.kmer_data[i] < kmer_data[i])
return false;
return false;
};
//-----------------------------------------------------------------------
// Return a symbol of a kmer from an indicated position (numbered form 0).
// The symbol is returned as an ASCI character A/C/G/T
// IN : pos - a position of a symbol
// RET : symbol - a symbol placed on a position pos
//-----------------------------------------------------------------------
inline char get_asci_symbol(unsigned int pos)
{
if(pos >= kmer_length)
return 0;
uint32 current_row = (pos + byte_alignment) / 32;
uint32 current_pos = ((pos + byte_alignment) % 32) * 2;
uint64 mask = 0xc000000000000000 >> current_pos;
uint64 symbol = kmer_data[current_row] & mask;
symbol = symbol >> (64 - current_pos - 2);
return char_codes[symbol];
};
//-----------------------------------------------------------------------
// Return a symbol of a kmer from an indicated position (numbered form 0)
// The symbol is returned as a numerical value 0/1/2/3
// IN : pos - a position of a symbol
// RET : symbol - a symbol placed on a position pos
//-----------------------------------------------------------------------
inline uchar get_num_symbol(unsigned int pos)
{
if (pos >= kmer_length)
return 0;
uint32 current_row = (pos + byte_alignment) / 32;
uint32 current_pos = ((pos + byte_alignment) % 32) * 2;
uint64 mask = 0xc000000000000000 >> current_pos;
uint64 symbol = kmer_data[current_row] & mask;
symbol = symbol >> (64 - current_pos - 2);
uchar* byte_ptr = reinterpret_cast<uchar*>(&symbol);
return *byte_ptr;
};
//-----------------------------------------------------------------------
// Convert kmer into string (an alphabet ACGT)
// RET : string kmer
//-----------------------------------------------------------------------
inline std::string to_string()
{
std::string string_kmer;
string_kmer.resize(kmer_length);
to_string_impl(string_kmer.begin());
return string_kmer;
};
//-----------------------------------------------------------------------
// Convert kmer into string (an alphabet ACGT). The function assumes enough memory was allocated
// OUT : str - string kmer.
//-----------------------------------------------------------------------
inline void to_string(char *str)
{
to_string_impl(str);
str[kmer_length] = '\0';
};
inline void to_long(std::vector<uint64>& kmer)
{
kmer.resize(no_of_rows);
uint32 offset = 62 - ((kmer_length - 1 + byte_alignment) & 31) * 2;
for (int32 i = no_of_rows - 1; i >= 1; --i)
{
kmer[i] = kmer_data[i] >> offset;
kmer[i] += kmer_data[i - 1] << (64 - offset);
}
kmer[0] = kmer_data[0] >> offset;
}
//-----------------------------------------------------------------------
// Convert kmer into string (an alphabet ACGT)
// OUT : str - string kmer
//-----------------------------------------------------------------------
inline void to_string(std::string &str)
{
str.resize(kmer_length);
to_string_impl(str.begin());
};
//-----------------------------------------------------------------------
// Convert a string of an alphabet ACGT into a kmer of a CKmerAPI
// IN : kmer_string - a string of an alphabet ACGT
// RET : true - if succesfull
//-----------------------------------------------------------------------
inline bool from_string(const char* kmer_string)
{
uint32 len = 0;
for (; kmer_string[len] != '\0' ; ++len)
{
if (num_codes[(uchar)kmer_string[len]] == -1)
return false;
}
return from_string_impl(kmer_string, len);
}
//-----------------------------------------------------------------------
// Convert a string of an alphabet ACGT into a kmer of a CKmerAPI
// IN : kmer_string - a string of an alphabet ACGT
// RET : true - if succesfull
//-----------------------------------------------------------------------
inline bool from_string(const std::string& kmer_string)
{
for (uint32 ii = 0; ii < kmer_string.size(); ++ii)
{
if (num_codes[(uchar)kmer_string[ii]] == -1)
return false;
}
return from_string_impl(kmer_string.begin(), static_cast<uint32>(kmer_string.length()));
}
//-----------------------------------------------------------------------
// Convert k-mer to its reverse complement
//-----------------------------------------------------------------------
inline bool reverse()
{
if (kmer_data == NULL)
{
return false;
}
// number of bytes used to store the k-mer in the 0-th row
const uint32 size_in_byte = ((kmer_length + byte_alignment) / 4) / no_of_rows;
uchar* byte1;
uchar* byte2;
if (no_of_rows == 1)
{
*kmer_data <<= 2 * byte_alignment;
byte1 = reinterpret_cast<uchar*>(kmer_data)+8 - size_in_byte;
byte2 = reinterpret_cast<uchar*>(kmer_data)+7;
for (uint32 i_bytes = 0; i_bytes < size_in_byte / 2; ++i_bytes)
{
unsigned char temp = rev_comp_bytes_LUT[*byte1];
*byte1 = rev_comp_bytes_LUT[*byte2];
*byte2 = temp;
++byte1;
--byte2;
}
if (size_in_byte % 2)
{
*byte1 = rev_comp_bytes_LUT[*byte1];
}
}
else
{
for (uint32 i_rows = no_of_rows - 1; i_rows > 0; --i_rows)
{
kmer_data[i_rows] >>= 64 - 8 * size_in_byte - 2 * byte_alignment;
// more significant row
uint64 previous = kmer_data[i_rows - 1];
previous <<= 8 * size_in_byte + 2 * byte_alignment;
kmer_data[i_rows] |= previous;
byte1 = reinterpret_cast<uchar*>(kmer_data + i_rows);
byte2 = reinterpret_cast<uchar*>(kmer_data + i_rows) + 7;
for (int i_bytes = 0; i_bytes < 4; ++i_bytes)
{
unsigned char temp = rev_comp_bytes_LUT[*byte1];
*byte1 = rev_comp_bytes_LUT[*byte2];
*byte2 = temp;
++byte1;
--byte2;
}
}
// clear less significant bits
kmer_data[0] >>= 64 - 8 * size_in_byte - 2 * byte_alignment;
kmer_data[0] <<= 64 - 8 * size_in_byte;
byte1 = reinterpret_cast<uchar*>(kmer_data)+8 - size_in_byte;
byte2 = reinterpret_cast<uchar*>(kmer_data)+7;
for (uint32 i_bytes = 0; i_bytes < size_in_byte / 2; ++i_bytes)
{
unsigned char temp = rev_comp_bytes_LUT[*byte1];
*byte1 = rev_comp_bytes_LUT[*byte2];
*byte2 = temp;
++byte1;
--byte2;
}
if (size_in_byte % 2)
{
*byte1 = rev_comp_bytes_LUT[*byte1];
}
for (uint32 i_rows = 0; i_rows < no_of_rows / 2; ++i_rows)
{
std::swap(kmer_data[i_rows], kmer_data[no_of_rows - i_rows - 1]);
}
}
// clear alignment
*kmer_data &= alignment_mask[byte_alignment];
return true;
}
//-----------------------------------------------------------------------
// Counts a signature of an existing kmer
// IN : sig_len - the length of a signature
// RET : signature value
//-----------------------------------------------------------------------
uint32 get_signature(uint32 sig_len)
{
uchar symb;
CMmer cur_mmr(sig_len);
for(uint32 i = 0; i < sig_len; ++i)
{
symb = get_num_symbol(i);
cur_mmr.insert(symb);
}
CMmer min_mmr(cur_mmr);
for (uint32 i = sig_len; i < kmer_length; ++i)
{
symb = get_num_symbol(i);
cur_mmr.insert(symb);
if (cur_mmr < min_mmr)
min_mmr = cur_mmr;
}
return min_mmr.get();
}
};
#endif
// ***** EOF
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