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Develop2 #164

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Develop2 #164

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95f2e8a
refactor makefile
danflomin Feb 7, 2021
e77c584
checkpoint before remote dev with vs code
danflomin Feb 11, 2021
94e81e3
implement uhs+frequency+signature ordering.
danflomin Feb 14, 2021
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63 changes: 33 additions & 30 deletions kmc_api/mmer.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -24,38 +24,41 @@ CMmer::_si CMmer::_init;


//--------------------------------------------------------------------------
CMmer::CMmer(uint32 _len)
CMmer::CMmer(uint32 _len, CMmerNorm* _norm)
{
switch (_len)
{
case 5:
norm = norm5;
break;
case 6:
norm = norm6;
break;
case 7:
norm = norm7;
break;
case 8:
norm = norm8;
break;
case 9:
norm = norm9;
break;
case 10:
norm = norm10;
break;
case 11:
norm = norm11;
break;
default:
break;
}
len = _len;
mask = (1 << _len * 2) - 1;
str = 0;
switch (_len)
{
case 5:
norm = norm5;
break;
case 6:
norm = norm6;
break;
case 7:
norm = norm7;
break;
case 8:
norm = norm8;
break;
case 9:
norm = norm9;
break;
case 10:
norm = norm10;
break;
case 11:
norm = norm11;
break;
default:
break;
}
len = _len;
mask = (1 << _len * 2) - 1;
str = 0;

new_norm = _norm;
}

//--------------------------------------------------------------------------

// ***** EOF
274 changes: 144 additions & 130 deletions kmc_api/mmer.h
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Original file line number Diff line number Diff line change
Expand Up @@ -18,180 +18,194 @@

class CMmer
{
uint32 str;
uint32 mask;
uint32 current_val;
uint32* norm;
uint32 len;
static uint32 norm5[1 << 10];
static uint32 norm6[1 << 12];
static uint32 norm7[1 << 14];
static uint32 norm8[1 << 16];
static uint32 norm9[1 << 18];
static uint32 norm10[1 << 20];
static uint32 norm11[1 << 22];

static bool is_allowed(uint32 mmer, uint32 len)
{
if ((mmer & 0x3f) == 0x3f) // TTT suffix
return false;
if ((mmer & 0x3f) == 0x3b) // TGT suffix
return false;
if ((mmer & 0x3c) == 0x3c) // TG* suffix !!!! consider issue #152
return false;

for (uint32 j = 0; j < len - 3; ++j)
if ((mmer & 0xf) == 0) // AA inside
return false;
else
mmer >>= 2;

if (mmer == 0) // AAA prefix
return false;
if (mmer == 0x04) // ACA prefix
return false;
if ((mmer & 0xf) == 0) // *AA prefix
return false;

return true;
}

friend class CSignatureMapper;
struct _si
{
static uint32 get_rev(uint32 mmer, uint32 len)
{
uint32 rev = 0;
uint32 shift = len*2 - 2;
for(uint32 i = 0 ; i < len ; ++i)
{
rev += (3 - (mmer & 3)) << shift;
mmer >>= 2;
shift -= 2;
}
return rev;
}



static void init_norm(uint32* norm, uint32 len)
{
uint32 special = 1 << len * 2;
for(uint32 i = 0 ; i < special ; ++i)
{
uint32 rev = get_rev(i, len);
uint32 str_val = is_allowed(i, len) ? i : special;
uint32 rev_val = is_allowed(rev, len) ? rev : special;
norm[i] = MIN(str_val, rev_val);
}
}

_si()
{
init_norm(norm5, 5);
init_norm(norm6, 6);
init_norm(norm7, 7);
init_norm(norm8, 8);
init_norm(norm9, 9);
init_norm(norm10, 10);
init_norm(norm11, 11);
}

}static _init;
uint32 str;
uint32 mask;
uint32 current_val;
uint32* norm;
uint32 len;

CMmerNorm* new_norm;

static uint32 norm5[1 << 10];
static uint32 norm6[1 << 12];
static uint32 norm7[1 << 14];
static uint32 norm8[1 << 16];
static uint32 norm9[1 << 18];
static uint32 norm10[1 << 20];
static uint32 norm11[1 << 22];

static bool is_allowed(uint32 mmer, uint32 len)
{
if ((mmer & 0x3f) == 0x3f) // TTT suffix
return false;
if ((mmer & 0x3f) == 0x3b) // TGT suffix
return false;
if ((mmer & 0x3c) == 0x3c) // TG* suffix !!!! consider issue #152
return false;

for (uint32 j = 0; j < len - 3; ++j)
if ((mmer & 0xf) == 0) // AA inside
return false;
else
mmer >>= 2;

if (mmer == 0) // AAA prefix
return false;
if (mmer == 0x04) // ACA prefix
return false;
if ((mmer & 0xf) == 0) // *AA prefix
return false;

return true;
}

friend class CSignatureMapper;
struct _si
{
static uint32 get_rev(uint32 mmer, uint32 len)
{
uint32 rev = 0;
uint32 shift = len*2 - 2;
for(uint32 i = 0 ; i < len ; ++i)
{
rev += (3 - (mmer & 3)) << shift;
mmer >>= 2;
shift -= 2;
}
return rev;
}



static void init_norm(uint32* norm, uint32 len)
{
uint32 special = 1 << len * 2;
for(uint32 i = 0 ; i < special ; ++i)
{
uint32 rev = get_rev(i, len);
uint32 str_val = is_allowed(i, len) ? i : special;
uint32 rev_val = is_allowed(rev, len) ? rev : special;
norm[i] = MIN(str_val, rev_val);
}
}

_si()
{
init_norm(norm5, 5);
init_norm(norm6, 6);
init_norm(norm7, 7);
init_norm(norm8, 8);
init_norm(norm9, 9);
init_norm(norm10, 10);
init_norm(norm11, 11);
}

}static _init;
public:
CMmer(uint32 _len);
inline void insert(uchar symb);
inline uint32 get() const;
inline bool operator==(const CMmer& x);
inline bool operator<(const CMmer& x);
inline void clear();
inline bool operator<=(const CMmer& x);
inline void set(const CMmer& x);
inline void insert(const char* seq);
CMmer(uint32 _len, CMmerNorm* _norm);
inline void insert(uchar symb);
inline uint32 get() const;
inline bool operator==(const CMmer& x);
inline bool operator<(const CMmer& x);
inline void clear();
inline bool operator<=(const CMmer& x);
inline void set(const CMmer& x);
inline void insert(const char* seq);

};



//--------------------------------------------------------------------------
inline void CMmer::insert(uchar symb)
{
str <<= 2;
str += symb;
str &= mask;
str <<= 2;
str += symb;
str &= mask;

current_val = norm[str];
current_val = norm[str];
}

//--------------------------------------------------------------------------
inline uint32 CMmer::get() const
{
return current_val;
return current_val;
}

//--------------------------------------------------------------------------
inline bool CMmer::operator==(const CMmer& x)
{
return current_val == x.current_val;
return current_val == x.current_val;
}

//--------------------------------------------------------------------------
inline bool CMmer::operator<(const CMmer& x)
{
return current_val < x.current_val;
return current_val < x.current_val;
}

//--------------------------------------------------------------------------
inline void CMmer::clear()
{
str = 0;
str = 0;
}

//--------------------------------------------------------------------------
inline bool CMmer::operator<=(const CMmer& x)
{
return current_val <= x.current_val;
return current_val <= x.current_val;
}

//--------------------------------------------------------------------------
inline void CMmer::set(const CMmer& x)
{
str = x.str;
current_val = x.current_val;
str = x.str;
current_val = x.current_val;
}

//--------------------------------------------------------------------------
inline void CMmer::insert(const char* seq)
{
switch (len)
{
case 5:
str = (seq[0] << 8) + (seq[1] << 6) + (seq[2] << 4) + (seq[3] << 2) + (seq[4]);
break;
case 6:
str = (seq[0] << 10) + (seq[1] << 8) + (seq[2] << 6) + (seq[3] << 4) + (seq[4] << 2) + (seq[5]);
break;
case 7:
str = (seq[0] << 12) + (seq[1] << 10) + (seq[2] << 8) + (seq[3] << 6) + (seq[4] << 4 ) + (seq[5] << 2) + (seq[6]);
break;
case 8:
str = (seq[0] << 14) + (seq[1] << 12) + (seq[2] << 10) + (seq[3] << 8) + (seq[4] << 6) + (seq[5] << 4) + (seq[6] << 2) + (seq[7]);
break;
case 9:
str = (seq[0] << 16) + (seq[1] << 14) + (seq[2] << 12) + (seq[3] << 10) + (seq[4] << 8) + (seq[5] << 6) + (seq[6] << 4) + (seq[7] << 2) + (seq[8]);
break;
case 10:
str = (seq[0] << 18) + (seq[1] << 16) + (seq[2] << 14) + (seq[3] << 12) + (seq[4] << 10) + (seq[5] << 8) + (seq[6] << 6) + (seq[7] << 4) + (seq[8] << 2) + (seq[9]);
break;
case 11:
str = (seq[0] << 20) + (seq[1] << 18) + (seq[2] << 16) + (seq[3] << 14) + (seq[4] << 12) + (seq[5] << 10) + (seq[6] << 8) + (seq[7] << 6) + (seq[8] << 4) + (seq[9] << 2) + (seq[10]);
break;
default:
break;
}

current_val = norm[str];
switch (len)
{
case 5:
str = (seq[0] << 8) + (seq[1] << 6) + (seq[2] << 4) + (seq[3] << 2) + (seq[4]);
break;
case 6:
str = (seq[0] << 10) + (seq[1] << 8) + (seq[2] << 6) + (seq[3] << 4) + (seq[4] << 2) + (seq[5]);
break;
case 7:
str = (seq[0] << 12) + (seq[1] << 10) + (seq[2] << 8) + (seq[3] << 6) + (seq[4] << 4 ) + (seq[5] << 2) + (seq[6]);
break;
case 8:
str = (seq[0] << 14) + (seq[1] << 12) + (seq[2] << 10) + (seq[3] << 8) + (seq[4] << 6) + (seq[5] << 4) + (seq[6] << 2) + (seq[7]);
break;
case 9:
str = (seq[0] << 16) + (seq[1] << 14) + (seq[2] << 12) + (seq[3] << 10) + (seq[4] << 8) + (seq[5] << 6) + (seq[6] << 4) + (seq[7] << 2) + (seq[8]);
break;
case 10:
str = (seq[0] << 18) + (seq[1] << 16) + (seq[2] << 14) + (seq[3] << 12) + (seq[4] << 10) + (seq[5] << 8) + (seq[6] << 6) + (seq[7] << 4) + (seq[8] << 2) + (seq[9]);
break;
case 11:
str = (seq[0] << 20) + (seq[1] << 18) + (seq[2] << 16) + (seq[3] << 14) + (seq[4] << 12) + (seq[5] << 10) + (seq[6] << 8) + (seq[7] << 6) + (seq[8] << 4) + (seq[9] << 2) + (seq[10]);
break;
default:
break;
}

if(norm == nullptr)
{
current_val = norm[str];
}
else
{
current_val = new_norm->get_norm_value(str);
}


}


#endif
#endif

// ***** EOF
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