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#include "Sequence.h"
#include "Common/Options.h"
#include <algorithm>
#include <cassert>
#include <cctype>
#include <cstdlib> // for abort
#include <iostream>
#include <sstream>
using namespace std;
enum { A, C, G, T };
static const int cstont[4][4] = {
{ A, C, G, T },
{ C, A, T, G },
{ G, T, A, C },
{ T, G, C, A }
};
/** Return the complement of the specified nucleotide. */
char complementBaseChar(char c)
{
char rc;
switch (toupper(c)) {
case 'A': rc = 'T'; break;
case 'C': rc = 'G'; break;
case 'G': rc = 'C'; break;
case 'T': rc = 'A'; break;
case 'N': rc = 'N'; break;
case '.': rc = '.'; break;
case 'M': rc = 'K'; break; // A or C
case 'R': rc = 'Y'; break; // A or G
case 'W': rc = 'W'; break; // A or T
case 'S': rc = 'S'; break; // C or G
case 'Y': rc = 'R'; break; // C or T
case 'K': rc = 'M'; break; // G or T
case 'V': rc = 'B'; break; // A or C or G
case 'H': rc = 'D'; break; // A or C or T
case 'D': rc = 'H'; break; // A or G or T
case 'B': rc = 'V'; break; // C or G or T
default:
cerr << "error: unexpected character: `" << c << "'\n";
assert(false);
abort();
}
return islower(c) ? tolower(rc) : rc;
}
/** Return the reverse complement of the specified sequence. */
Sequence reverseComplement(const Sequence& s)
{
Sequence rc(s);
reverse(rc.begin(), rc.end());
if (!opt::colourSpace)
transform(rc.begin(), rc.end(), rc.begin(),
complementBaseChar);
return rc;
}
static const uint8_t b2C[256] = {
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //0
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //1
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //2
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0x00, 0x01, 0x02, 0x03, 0xFF, 0xFF, 0xFF, 0xFF, //3 0 1 2 3
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0x00, 0xFF, 0x01, 0xFF, 0xFF, 0xFF, 0x02, //4 A C G
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0x03, 0xFF, 0xFF, 0xFF, //5 T
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0x00, 0xFF, 0x01, 0xFF, 0xFF, 0xFF, 0x02, //6 a c g
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0x03, 0xFF, 0xFF, 0xFF, //7 t
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //8
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //9
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //A
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //B
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //C
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //D
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //E
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF,
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, //F
0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF
};
/** Return the base enumeration for the specified character. */
uint8_t baseToCode(char base)
{
uint8_t r = b2C[unsigned(base)];
if (r != 0xFF) return r;
cerr << "error: unexpected character: '"
<< base << "'\n";
assert(false);
abort();
}
char codeToBase(uint8_t code)
{
assert(code < 4);
return (opt::colourSpace ? "0123" : "ACGT")[code];
}
char colourToNucleotideSpace(char anchor, char cs)
{
return cs == '.' ? 'N'
: "ACGT"[cstont[baseToCode(anchor)][baseToCode(cs)]];
}
Sequence colourToNucleotideSpace(char anchor, const Sequence& seq)
{
int seed = baseToCode(anchor);
ostringstream s;
s << anchor;
for (string::const_iterator it = seq.begin();
it != seq.end(); ++it) {
seed = cstont[seed][baseToCode(*it)];
s << codeToBase(seed);
}
return s.str();
}
char nucleotideToColourSpace(char a, char b)
{
if (toupper(a) == 'N' || toupper(b) == 'N')
return islower(a) || islower(b) ? 'n' : 'N';
return "0123"[cstont[baseToCode(a)][baseToCode(b)]];
}
/** Convert the specified ambiguity code to a bitmask. */
unsigned ambiguityToBitmask(char c)
{
if (isdigit(c)) // colour space
return 1 << baseToCode(c);
static const unsigned ambiguityToBitmaskTable[26] = {
0x1, // 'A' ---A
0xe, // 'B' TGC-
0x2, // 'C' --C-
0xd, // 'D' TG-A
0x0, // 'E'
0x0, // 'F'
0x4, // 'G' -G--
0xb, // 'H' T-CA
0x0, // 'I'
0x0, // 'J'
0xc, // 'K' TG--
0x0, // 'L'
0x3, // 'M' --CA
0xf, // 'N' ACGT
0x0, // 'O'
0x0, // 'P'
0x0, // 'Q'
0x5, // 'R' -G-A
0x6, // 'S' -GC-
0x8, // 'T' T---
0x0, // 'U'
0x7, // 'V' -GCA
0x9, // 'W' T--A
0x0, // 'X'
0xa, // 'Y' T-C-
0x0, // 'Z'
};
unsigned i = toupper(c) - 'A';
assert(i < 26);
unsigned x = ambiguityToBitmaskTable[i];
assert(x > 0);
return x;
}
/** Convert the specified bitmask to an ambiguity code. */
unsigned bitmaskToAmbiguity(unsigned x)
{
static const char bitmaskToAmbiguityTable[16] = {
'N', //----
'A', //---A
'C', //--C-
'M', //--CA
'G', //-G--
'R', //-G-A
'S', //-GC-
'V', //-GCA
'T', //T---
'W', //T--A
'Y', //T-C-
'H', //T-CA
'K', //TG--
'D', //TG-A
'B', //TGC-
'N', //TGCA
};
assert(x < 16);
return bitmaskToAmbiguityTable[x];
}
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