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defs01.h
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#ifndef GAURD_defs01
#define GAURD_defs01
#define NUMBER_OF_PREFIXES 9
#define LOG_2 0.6931471805599453
#define A_prior 1.01
#define B_prior 1.01
#define D_prior 1.01
#define THRESHOLD 1e-10
#define MAX_ITER 500
#define MUTATION_RATE 1e-11
////////////////
struct initialization_info {
int CHROM_col, POS_col, ID_col, REF_col, ALT_col, QUAL_col, FILTER_col, INFO_col, FORMAT_col;
int sample_count;
initialization_info(std::string &);
void set_header_info(const std::string &);
};
std::ostream & operator << (std::ostream & out, const initialization_info & O) {
using namespace std;
out<< "initialization_info:\n";
out<< "********************\n";
cout<< "CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT"<<"\n";
cout<< O.CHROM_col <<"\t"<< O.POS_col <<"\t"<< O.ID_col <<"\t"<< O.REF_col <<"\t"<< O.ALT_col <<"\t"<< O.QUAL_col <<"\t"<< O.FILTER_col <<"\t"<< O.INFO_col <<"\t"<< O.FORMAT_col <<"\n";
cout<< "sample_count = " << O.sample_count <<"\n";
return out;
}
initialization_info::initialization_info(std::string & line) {
set_header_info(line);
}
void initialization_info::set_header_info(const std::string & header_line) {
using namespace std;
CHROM_col = POS_col = ID_col = REF_col = ALT_col = QUAL_col = FILTER_col = INFO_col = FORMAT_col = -1;
const vector<string> SL( split(header_line) );
for(size_t i(0) ; i < SL.size() ; ++i) {
if(SL[i] == "#CHROM")
CHROM_col = i;
if(SL[i] == "POS")
POS_col = i;
if(SL[i] == "ID")
ID_col = i;
if(SL[i] == "REF")
REF_col = i;
if(SL[i] == "ALT")
ALT_col = i;
if(SL[i] == "QUAL")
QUAL_col = i;
if(SL[i] == "FILTER")
FILTER_col = i;
if(SL[i] == "INFO")
INFO_col = i;
if(SL[i] == "FORMAT")
FORMAT_col = i;
}
sample_count = SL.size() - NUMBER_OF_PREFIXES;
}
////////////////
struct AD_info {
thrust::host_vector<int> AD0, AD1;
thrust::device_vector<int> DAD0,DAD1;
int FORMAT_length, AD_position, CHROM, POS;
AD_info(const initialization_info &);
bool read_once(std::istream &, const initialization_info &);
void FORMAT_info_extract(const std::string &);
void CHROM_extract(const std::string &);
std::string integer_to_chromosome() const;
void POS_extract(const std::string &);
};
std::string AD_info::integer_to_chromosome() const {
using namespace std;
string temp;
if(CHROM == 0)
temp = string("M");
else
if(CHROM == 23)
temp = string("X");
else
if(CHROM == 24)
temp = string("Y");
else
temp = myitoa(CHROM);
const string ans(string("chr") + temp);
return ans;
}
void AD_info::POS_extract(const std::string & S) {
using namespace std;
POS = atoi( S.c_str() );
}
void AD_info::CHROM_extract(const std::string & S) {
using namespace std;
string S_temp, S2;
if(S.size() > 3)
S_temp = string(S.begin(), S.begin() + 3);
else
S_temp=S;
if(S_temp == "chr")
S2 = string(S.begin() + 3, S.end());
else
S2=S;
const int num( atoi( S2.c_str() ) );
if(num >= 1 and num <= 22)
CHROM = num;
else
if(S2 == "M" or S2 == "m")
CHROM = 0;
else
if(S2 == "X" or S2 == "x")
CHROM = 23;
else
if(S2 == "Y" or S2 == "y")
CHROM = 24;
else
throw(domain_error("ERROR in CHROM_extract"));
}
std::ostream & operator << (std::ostream & out, const AD_info & O) {
using namespace std;
out<< "AD_info:\n";
out<< "********\n";
cout<< "AD_position = " << O.AD_position <<"\n";
cout<< "FORMAT_length = " << O.FORMAT_length <<"\n";
cout<< "CHROM, POS = "<< O.CHROM <<", "<< O.POS <<"\n";
if(O.AD0.size() != O.AD1.size() or O.DAD0.size() != O.DAD1.size() or O.AD0.size() != O.DAD0.size() )
throw(domain_error("ERROR in operator << (std::ostream & out, const AD_info & O)"));
for(int i(0) ; i < O.AD0.size() ; ++i)
cout<< i << ")\t" << O.AD0[i] <<"\t"<< O.AD1[i] <<"\t"<< O.DAD0[i] <<"\t"<< O.DAD1[i] <<"\n";
return out;
}
AD_info::AD_info(const initialization_info & IIO) {
using namespace thrust;
AD0 = host_vector<int>(IIO.sample_count);
AD1 = host_vector<int>(IIO.sample_count);
DAD0 = device_vector<int>(IIO.sample_count);
DAD1 = device_vector<int>(IIO.sample_count);
}
void AD_info::FORMAT_info_extract(const std::string & FORMAT) {
using namespace std;
AD_position = FORMAT_length = -1;
const vector<string> SL( split(FORMAT, ":") );
FORMAT_length = SL.size();
for(int i(0) ; i < SL.size() ; ++i)
if(SL[i] == "AD")
AD_position = i;
if(AD_position == -1 or FORMAT_length == -1)
throw(domain_error("ERROR in AD_info::AD_info_extract"));
}
bool AD_info::read_once(std::istream & fin, const initialization_info & IIO) {
std::string temp;
for(int i(0) ; i < NUMBER_OF_PREFIXES ; ++i) {
fin >> temp;
if(not fin)
return false;
if(i == IIO.FORMAT_col)
FORMAT_info_extract(temp);
if(i == IIO.CHROM_col)
CHROM_extract(temp);
if(i == IIO.POS_col)
POS_extract(temp);
}
for(int i(0) ; i < AD0.size() ; ++i) {
fin >> temp;
std::vector<std::string> SL( split(temp, ":") );
if(SL.size() != FORMAT_length) {
AD0[i] = 0;
AD1[i] = 0;
continue;
}
temp = SL[AD_position];
SL = split(temp, ",");
if(SL.size() <= 1) {
AD0[i] = 0;
AD1[i] = 0;
continue;
}
AD0[i] = atoi( SL[0].c_str() );
AD1[i] = 0;
for(int j(1) ; j < SL.size() ; ++j)
AD1[i] += atoi( SL[j].c_str() );
}
thrust::copy(AD0.begin(), AD0.end(), DAD0.begin());
thrust::copy(AD1.begin(), AD1.end(), DAD1.begin());
return true;
}
////////////////
struct sample_info {
std::vector<int> control_index;
std::vector<std::vector<int> > trios;
std::vector<std::string> sample_names;
thrust::device_vector<int> device_control_index;
thrust::device_vector<int> device_P1_index;
thrust::device_vector<int> device_P2_index;
thrust::device_vector<int> device_child_index;
sample_info(const std::string & header_line, const std::string & control_filename, const std::string & trio_filename);
int find_in_line(const std::string &, const std::vector<std::string> &);
};
std::ostream & operator << (std::ostream & out, const sample_info & O) {
using namespace std;
out<< "sample_info:\n";
out<< "************\n";
out<< "control_index:\n";
out<< O.control_index <<"\t:"<< "number_of_control = "<< O.control_index.size() <<"\n";
out<< "device_control_index:\n";
out<< O.device_control_index <<"\t:"<< "number_of_control = "<< O.device_control_index.size() <<"\n";
out<< "trios:\n";
for(int i(0);i<O.trios.size();++i)
out<< O.trios[i] <<"\n";
out<< "number of trios = " << O.trios.size() <<"\n";
out<< "device_trio_indexes:\n";
out<< O.device_P1_index <<"\t"<< "length = " << O.device_P1_index.size() <<"\n";
out<< O.device_P2_index <<"\t"<< "length = " << O.device_P2_index.size() <<"\n";
out<< O.device_child_index <<"\t"<< "length = " << O.device_child_index.size() <<"\n";
for(int i(0);i<O.sample_names.size();++i)
out<< i <<") "<< O.sample_names[i] <<"\t";
out<< ":no_of_samples = "<< O.sample_names.size() <<"\n";
return out;
}
int sample_info::find_in_line(const std::string & temp, const std::vector<std::string> & SL) {
using namespace std;
for(int i(NUMBER_OF_PREFIXES) ; i < SL.size() ; ++i)
if(SL[i] == temp)
return (i - NUMBER_OF_PREFIXES);
throw(domain_error("ERROR01 in sample_info::find_in_line"));
}
sample_info::sample_info(const std::string & header_line, const std::string & control_filename, const std::string & trio_filename) {
using namespace std;
control_index = vector<int>(0);
trios = vector<vector<int> >(0);
const vector<string> SL( split(header_line) );
sample_names = vector<string>(SL.begin() + NUMBER_OF_PREFIXES, SL.end());
ifstream fincontrol( control_filename.c_str() );
if(not fincontrol)
throw(domain_error("ERROR01 in sample_info::sample_info: control file does not exist"));
string temp;
fincontrol >> temp;
while(fincontrol) {
control_index.push_back( find_in_line(temp, SL));
fincontrol >> temp;
}
sort(control_index.begin(), control_index.end());
fincontrol.close();
ifstream fintrio(trio_filename.c_str());
if(not fintrio)
throw(domain_error("ERROR02 in sample_info::sample_info: trio file does not exist"));
getline(fintrio, temp);
while(fintrio) {
const vector<string> split_temp( split(temp) );
if(split_temp.size() != 3)
throw(domain_error("ERROR03 in sample_info::sample_info: trio file inconsistent format"));
vector<int> row(0);
for(int i(0);i<3;++i)
row.push_back( find_in_line(split_temp[i], SL) );
trios.push_back( row );
getline(fintrio, temp);
}
fintrio.close();
device_control_index = thrust::device_vector<int>(control_index.size());
thrust::copy(control_index.begin(), control_index.end(), device_control_index.begin());
device_P1_index = thrust::device_vector<int>( trios.size() );
device_P2_index = thrust::device_vector<int>( trios.size() );
device_child_index = thrust::device_vector<int>( trios.size() );
for(int i(0);i<trios.size();++i) {
device_P1_index[i] = trios[i][0];
device_P2_index[i] = trios[i][1];
device_child_index[i] = trios[i][2];
}
}
////////////////
struct EM_worker {
double rho, lhood, lhood_prev;
std::vector<double> F;
size_t iters;
char set_by; // -1 when initialized or reset, 0 when set by GPU computation, 1 when set by CPU computation.
EM_worker();
void reset();
void EM_step (const AD_info &, const sample_info &);
void EM_step_CPU(const AD_info &, const sample_info &);
void EM_full (const AD_info &, const sample_info &);
void EM_full_CPU(const AD_info &, const sample_info &);
};
std::ostream & operator << (std::ostream & out, const EM_worker & O) {
using namespace std;
out<< "EM_worker:\n";
out<< "**********\n";
if(O.set_by == -1) {
out<< "initialized or reset\n";
out<< "--------------------\n";
}
else
if(O.set_by == 0) {
out<< "set by GPU\n";
out<< "----------\n";
}
else
if(O.set_by == 1) {
out<< "set by CPU\n";
out<< "----------\n";
}
else
throw(domain_error("ERROR in displaying EM_worker"));
out<< "rho = " << O.rho <<"\n";
out<< "lhood_prev = " << O.lhood_prev <<"\n";
out<< "lhood = " << O.lhood <<"\n";
out<< "F: "<< O.F <<"\tsum = "<< SUM(O.F) <<"\n";
out<< "iters = " << O.iters <<"\n";
return out;
}
EM_worker::EM_worker() {
reset();
}
void EM_worker::reset() {
using namespace std;
rho = 0.7;
lhood = 0.0;
lhood_prev = 0.0;
F = vector<double>(3, 1.0/3.0);
iters = 0;
set_by = -1;
}
struct unary_op {
double rho;
double F0, F1, F2;
double log_rho, log_1_rho;
double logF0, logF1, logF2;
unary_op(const double & _rho, const double & _F0, const double & _F1, const double & _F2) {
rho = _rho;
F0 = _F0;
F1 = _F1;
F2 = _F2;
log_rho = log(rho);
log_1_rho = log(1.0 - rho);
logF0 = log(F0);
logF1 = log(F1);
logF2 = log(F2);
}
__host__ __device__
thrust::tuple<double, double, double, double, double, double> operator () (const thrust::tuple<int, int> & DAD) const {
if( thrust::get<0>(DAD) != 0 or thrust::get<1>(DAD) != 0) {
double log_w0( thrust::get<0>(DAD)*log_rho + thrust::get<1>(DAD)*log_1_rho + logF0 );
double log_w1( -( thrust::get<0>(DAD) + thrust::get<1>(DAD) )*LOG_2 + logF1 );
double log_w2( thrust::get<0>(DAD)*log_1_rho + thrust::get<1>(DAD)*log_rho + logF2 );
double max_val;
if(log_w0 > log_w1)
if(log_w0 > log_w2)
max_val = log_w0;
else
max_val = log_w2;
else
if(log_w1 > log_w2)
max_val = log_w1;
else
max_val = log_w2;
log_w0 -= max_val;
log_w1 -= max_val;
log_w2 -= max_val;
double w0( exp(log_w0) );
double w1( exp(log_w1) );
double w2( exp(log_w2) );
const double den( w0 + w1 + w2 );
const double log_lhood_term( log(den) + max_val );
w0 = w0 / den;
w1 = w1 / den;
w2 = w2 / den;
const double T1_term( w0*thrust::get<0>(DAD) + w2*thrust::get<1>(DAD) );
const double T2_term( w2*thrust::get<0>(DAD) + w0*thrust::get<1>(DAD) );
const thrust::tuple<double, double, double, double, double, double> ans( thrust::make_tuple(T1_term, T2_term, w0, w1, w2, log_lhood_term) );
return ans;
}
else {
const double w0( 0 );
const double w1( 0 );
const double w2( 0 );
const double T1_term( 0 );
const double T2_term( 0 );
const double log_lhood_term( 0 );
const thrust::tuple<double, double, double, double, double, double> ans( thrust::make_tuple(T1_term, T2_term, w0, w1, w2, log_lhood_term) );
return ans;
}
}
};
struct binary_op {
__host__ __device__
thrust::tuple<double, double, double, double, double, double> operator () (const thrust::tuple<double, double, double, double, double, double> & X, const thrust::tuple<double, double, double, double, double, double> & Y) const {
const double val0( thrust::get<0>(X) + thrust::get<0>(Y) );
const double val1( thrust::get<1>(X) + thrust::get<1>(Y) );
const double val2( thrust::get<2>(X) + thrust::get<2>(Y) );
const double val3( thrust::get<3>(X) + thrust::get<3>(Y) );
const double val4( thrust::get<4>(X) + thrust::get<4>(Y) );
const double val5( thrust::get<5>(X) + thrust::get<5>(Y) );
thrust::tuple<double, double, double, double, double, double> ans( thrust::make_tuple(val0, val1, val2, val3, val4, val5) );
return ans;
}
};
void EM_worker::EM_step(const AD_info & ADIO, const sample_info & SIO) {
typedef thrust::device_vector<int>::const_iterator map_iter;
typedef thrust::device_vector<int>::const_iterator source_iter;
typedef thrust::permutation_iterator<source_iter, map_iter> perm_iter;
perm_iter beg0 ( ADIO.DAD0.begin(), SIO.device_control_index.begin() );
perm_iter beg1 ( ADIO.DAD1.begin(), SIO.device_control_index.begin() );
perm_iter ender0 ( ADIO.DAD0.end() , SIO.device_control_index.end() );
perm_iter ender1 ( ADIO.DAD1.end() , SIO.device_control_index.end() );
typedef thrust::tuple<perm_iter, perm_iter> iter_tuple;
typedef thrust::zip_iterator<iter_tuple> zip_iter;
const zip_iter zip_beg ( thrust::make_zip_iterator( thrust::make_tuple(beg0 , beg1 ) ) );
const zip_iter zip_ender( thrust::make_zip_iterator( thrust::make_tuple(ender0, ender1) ) );
const unary_op UO(rho, F[0], F[1], F[2]);
const binary_op BO;
const double lhood_prior_term( (A_prior - 1.0)*log(rho) + (B_prior - 1.0)*log(1.0 - rho) + (D_prior - 1.0)*( log(F[0]) + log(F[1]) + log(F[2]) ) );
const thrust::tuple<double, double, double, double, double, double> init_val (A_prior - 1.0, B_prior - 1.0, D_prior - 1.0, D_prior - 1.0, D_prior - 1.0, lhood_prior_term);
const thrust::tuple<double, double, double, double, double, double> TS_VALS( thrust::transform_reduce(zip_beg, zip_ender, UO, init_val, BO) );
const double T1( thrust::get<0>( TS_VALS ) );
const double T2( thrust::get<1>( TS_VALS ) );
double F0( thrust::get<2>( TS_VALS ) );
double F1( thrust::get<3>( TS_VALS ) );
double F2( thrust::get<4>( TS_VALS ) );
const double den( F0 + F1 + F2 );
F0 = F0 / den;
F1 = F1 / den;
F2 = F2 / den;
rho = 1.0/( T2/T1 + 1.0);
F[0] = F0;
F[1] = F1;
F[2] = F2;
lhood_prev = lhood;
lhood = thrust::get<5>(TS_VALS);
}
void EM_worker::EM_step_CPU(const AD_info & ADIO, const sample_info & SIO) {
using namespace std;
const thrust::host_vector<int> &AD0( ADIO.AD0 ), &AD1( ADIO.AD1 ), &index( SIO.control_index );
const double lhood_prior_term( (A_prior - 1.0)*log(rho) + (B_prior - 1.0)*log(1.0 - rho) + (D_prior - 1.0)*( log(F[0]) + log(F[1]) + log(F[2]) ) );
double T1(A_prior - 1.0), T2(B_prior - 1.0), F0(D_prior - 1.0), F1(D_prior - 1.0), F2(D_prior - 1.0);
lhood_prev = lhood;
lhood = lhood_prior_term;
for(int i(0);i<index.size();++i) {
const int K( index[i] );
if(AD0[K] != 0 or AD1[K] != 0) {
double log_w0( AD0[K]*log(rho) + AD1[K]*log(1.0 - rho) + log( F[0] ));
double log_w1( -(AD0[K] + AD1[K])*LOG_2 + log( F[1] ) );
double log_w2( AD1[K]*log(rho) + AD0[K]*log(1.0 - rho) + log( F[2] ));
double max_val;
if(log_w0 > log_w1)
if(log_w0 > log_w2)
max_val = log_w0;
else
max_val = log_w2;
else
if(log_w1 > log_w2)
max_val = log_w1;
else
max_val = log_w2;
log_w0 -= max_val;
log_w1 -= max_val;
log_w2 -= max_val;
double w0( exp(log_w0) );
double w1( exp(log_w1) );
double w2( exp(log_w2) );
const double den( w0 + w1 + w2 );
lhood += ( log(den) + max_val );
w0 = w0 / den;
w1 = w1 / den;
w2 = w2 / den;
const double T1_term( w0*AD0[K] + w2*AD1[K] );
const double T2_term( w2*AD0[K] + w0*AD1[K] );
T1 += T1_term;
T2 += T2_term;
F0 += w0;
F1 += w1;
F2 += w2;
}
else {
T1 += 0.0;
T2 += 0.0;
F0 += 0.0;
F1 += 0.0;
F2 += 0.0;
lhood += 0.0;
}
}
const double den( F0 + F1 + F2 );
F0 = F0 / den;
F1 = F1 / den;
F2 = F2 / den;
rho = 1.0/( T2/T1 + 1.0);
F[0] = F0;
F[1] = F1;
F[2] = F2;
}
void EM_worker::EM_full(const AD_info & ADIO, const sample_info & SIO) {
reset();
EM_step(ADIO, SIO);
EM_step(ADIO, SIO);
iters = 2;
while(abs(lhood - lhood_prev) > THRESHOLD) {
EM_step(ADIO, SIO);
iters += 1;
if(iters > MAX_ITER)
break;
}
set_by = 0;
}
void EM_worker::EM_full_CPU(const AD_info & ADIO, const sample_info & SIO) {
reset();
EM_step_CPU(ADIO, SIO);
EM_step_CPU(ADIO, SIO);
iters = 2;
while(abs(lhood - lhood_prev) > THRESHOLD) {
EM_step_CPU(ADIO, SIO);
iters += 1;
if(iters > MAX_ITER)
break;
}
set_by = 1;
}
//////////////////
struct conditional_probty_table {
std::vector<double> CPT; // conditional_probty_table
thrust::device_vector<double> device_CPT; // GPU memory conditional_probty_table
std::vector<double> LOG_CPT; // log of conditional_probty_table
thrust::device_vector<double> device_LOG_CPT; // GPU memory log of conditional_probty_table
conditional_probty_table();
};
conditional_probty_table::conditional_probty_table() {
double temp[] = {1,0,0, 0.5,0.5,0, 0,1,0, 0.5,0.5,0, 0.25,0.5,0.25, 0,0.5,0.5, 0,1,0, 0,0.5,0.5, 0,0,1};
CPT = std::vector<double>(temp, temp + 27);
CPT += MUTATION_RATE;
LOG_CPT = LOG_1D(CPT);
device_CPT = thrust::device_vector<double>( CPT );
device_LOG_CPT = thrust::device_vector<double>( LOG_CPT );
}
std::ostream & operator << (std::ostream & out, const conditional_probty_table & O) {
out << "conditional_probty_table:\n";
out << "*************************\n";
out << "CPT:\n";
out << O.CPT <<"\t"<< ":length = "<< O.CPT.size() <<"\n";
out << "LOG_CPT:\n";
out << O.LOG_CPT <<"\t"<< ":length = "<< O.LOG_CPT.size() <<"\n";
out << "device_CPT:\n";
out << O.device_CPT <<"\t"<< ":length = "<< O.device_CPT.size() <<"\n";
out << "device_LOG_CPT:\n";
out << O.device_LOG_CPT <<"\t"<< ":length = "<< O.device_LOG_CPT.size() <<"\n";
return out;
}
//////////////////
struct caller_unary_op {
double CPTL000, CPTL001, CPTL002, CPTL010, CPTL011, CPTL012, CPTL020, CPTL021, CPTL022, CPTL100, CPTL101, CPTL102, CPTL110, CPTL111, CPTL112, CPTL120, CPTL121, CPTL122, CPTL200, CPTL201, CPTL202, CPTL210, CPTL211, CPTL212, CPTL220, CPTL221, CPTL222;
double rho;
double F0, F1, F2;
caller_unary_op(const conditional_probty_table & O, const double & _rho, const std::vector<double> & _F);
__host__ __device__
double operator () (const thrust::tuple<int, int, int, int, int, int> & X) const;
};
caller_unary_op::caller_unary_op(const conditional_probty_table & O, const double & _rho, const std::vector<double> & _F) {
if(O.LOG_CPT.size() != 27)
throw(std::domain_error("ERROR in caller_unary_op::caller_unary_op"));
CPTL000 = O.LOG_CPT[0];
CPTL001 = O.LOG_CPT[1];
CPTL002 = O.LOG_CPT[2];
CPTL010 = O.LOG_CPT[3];
CPTL011 = O.LOG_CPT[4];
CPTL012 = O.LOG_CPT[5];
CPTL020 = O.LOG_CPT[6];
CPTL021 = O.LOG_CPT[7];
CPTL022 = O.LOG_CPT[8];
CPTL100 = O.LOG_CPT[9];
CPTL101 = O.LOG_CPT[10];
CPTL102 = O.LOG_CPT[11];
CPTL110 = O.LOG_CPT[12];
CPTL111 = O.LOG_CPT[13];
CPTL112 = O.LOG_CPT[14];
CPTL120 = O.LOG_CPT[15];
CPTL121 = O.LOG_CPT[16];
CPTL122 = O.LOG_CPT[17];
CPTL200 = O.LOG_CPT[18];
CPTL201 = O.LOG_CPT[19];
CPTL202 = O.LOG_CPT[20];
CPTL210 = O.LOG_CPT[21];
CPTL211 = O.LOG_CPT[22];
CPTL212 = O.LOG_CPT[23];
CPTL220 = O.LOG_CPT[24];
CPTL221 = O.LOG_CPT[25];
CPTL222 = O.LOG_CPT[26];
rho = _rho;
F0 = _F[0];
F1 = _F[1];
F2 = _F[2];
}
double caller_unary_op::operator () (const thrust::tuple<int, int, int, int, int, int> & X) const {
// parent1 ADs, parent2 ADs, child ADs in that order
const int P1_AD0( thrust::get<0>(X) );
const int P1_AD1( thrust::get<1>(X) );
const int P2_AD0( thrust::get<2>(X) );
const int P2_AD1( thrust::get<3>(X) );
const int child_AD0( thrust::get<4>(X) );
const int child_AD1( thrust::get<5>(X) );
thrust::tuple<double, double, double> P1L, P2L, childL;
{
thrust::get<0>(P1L) = P1_AD0*log(rho) + P1_AD1*log(1.0 - rho);
thrust::get<1>(P1L) = -(P1_AD0 + P1_AD1)*LOG_2;
thrust::get<2>(P1L) = P1_AD1*log(rho) + P1_AD0*log(1.0 - rho);
thrust::get<0>(P2L) = P2_AD0*log(rho) + P2_AD1*log(1.0 - rho);
thrust::get<1>(P2L) = -(P2_AD0 + P2_AD1)*LOG_2;
thrust::get<2>(P2L) = P2_AD1*log(rho) + P2_AD0*log(1.0 - rho);
thrust::get<0>(childL) = child_AD0*log(rho) + child_AD1*log(1.0 - rho);
thrust::get<1>(childL) = -(child_AD0 + child_AD1)*LOG_2;
thrust::get<2>(childL) = child_AD1*log(rho) + child_AD0*log(1.0 - rho);
}
double PP000, PP001, PP002, PP010, PP011, PP012, PP020, PP021, PP022, PP100, PP101, PP102, PP110, PP111, PP112, PP120, PP121, PP122, PP200, PP201, PP202, PP210, PP211, PP212, PP220, PP221, PP222;
PP000 = CPTL000 + thrust::get<0>(P1L) + thrust::get<0>(P2L) + thrust::get<0>(childL);
PP001 = CPTL001 + thrust::get<0>(P1L) + thrust::get<0>(P2L) + thrust::get<1>(childL);
PP002 = CPTL002 + thrust::get<0>(P1L) + thrust::get<0>(P2L) + thrust::get<2>(childL);
PP010 = CPTL010 + thrust::get<0>(P1L) + thrust::get<1>(P2L) + thrust::get<0>(childL);
PP011 = CPTL011 + thrust::get<0>(P1L) + thrust::get<1>(P2L) + thrust::get<1>(childL);
PP012 = CPTL012 + thrust::get<0>(P1L) + thrust::get<1>(P2L) + thrust::get<2>(childL);
PP020 = CPTL020 + thrust::get<0>(P1L) + thrust::get<2>(P2L) + thrust::get<0>(childL);
PP021 = CPTL021 + thrust::get<0>(P1L) + thrust::get<2>(P2L) + thrust::get<1>(childL);
PP022 = CPTL022 + thrust::get<0>(P1L) + thrust::get<2>(P2L) + thrust::get<2>(childL);
PP100 = CPTL100 + thrust::get<1>(P1L) + thrust::get<0>(P2L) + thrust::get<0>(childL);
PP101 = CPTL101 + thrust::get<1>(P1L) + thrust::get<0>(P2L) + thrust::get<1>(childL);
PP102 = CPTL102 + thrust::get<1>(P1L) + thrust::get<0>(P2L) + thrust::get<2>(childL);
PP110 = CPTL110 + thrust::get<1>(P1L) + thrust::get<1>(P2L) + thrust::get<0>(childL);
PP111 = CPTL111 + thrust::get<1>(P1L) + thrust::get<1>(P2L) + thrust::get<1>(childL);
PP112 = CPTL112 + thrust::get<1>(P1L) + thrust::get<1>(P2L) + thrust::get<2>(childL);
PP120 = CPTL120 + thrust::get<1>(P1L) + thrust::get<2>(P2L) + thrust::get<0>(childL);
PP121 = CPTL121 + thrust::get<1>(P1L) + thrust::get<2>(P2L) + thrust::get<1>(childL);
PP122 = CPTL122 + thrust::get<1>(P1L) + thrust::get<2>(P2L) + thrust::get<2>(childL);
PP200 = CPTL200 + thrust::get<2>(P1L) + thrust::get<0>(P2L) + thrust::get<0>(childL);
PP201 = CPTL201 + thrust::get<2>(P1L) + thrust::get<0>(P2L) + thrust::get<1>(childL);
PP202 = CPTL202 + thrust::get<2>(P1L) + thrust::get<0>(P2L) + thrust::get<2>(childL);
PP210 = CPTL210 + thrust::get<2>(P1L) + thrust::get<1>(P2L) + thrust::get<0>(childL);
PP211 = CPTL211 + thrust::get<2>(P1L) + thrust::get<1>(P2L) + thrust::get<1>(childL);
PP212 = CPTL212 + thrust::get<2>(P1L) + thrust::get<1>(P2L) + thrust::get<2>(childL);
PP220 = CPTL220 + thrust::get<2>(P1L) + thrust::get<2>(P2L) + thrust::get<0>(childL);
PP221 = CPTL221 + thrust::get<2>(P1L) + thrust::get<2>(P2L) + thrust::get<1>(childL);
PP222 = CPTL222 + thrust::get<2>(P1L) + thrust::get<2>(P2L) + thrust::get<2>(childL);
double maxval( PP000 );
if(maxval < PP000)
maxval = PP000;
if(maxval < PP001)
maxval = PP001;
if(maxval < PP002)
maxval = PP002;
if(maxval < PP010)
maxval = PP010;
if(maxval < PP011)
maxval = PP011;
if(maxval < PP012)
maxval = PP012;
if(maxval < PP020)
maxval = PP020;
if(maxval < PP021)
maxval = PP021;
if(maxval < PP022)
maxval = PP022;
if(maxval < PP100)
maxval = PP100;
if(maxval < PP101)
maxval = PP101;
if(maxval < PP102)
maxval = PP102;
if(maxval < PP110)
maxval = PP110;
if(maxval < PP111)
maxval = PP111;
if(maxval < PP112)
maxval = PP112;
if(maxval < PP120)
maxval = PP120;
if(maxval < PP121)
maxval = PP121;
if(maxval < PP122)
maxval = PP122;
if(maxval < PP200)
maxval = PP200;
if(maxval < PP201)
maxval = PP201;
if(maxval < PP202)
maxval = PP202;
if(maxval < PP210)
maxval = PP210;
if(maxval < PP211)
maxval = PP211;
if(maxval < PP212)
maxval = PP212;
if(maxval < PP220)
maxval = PP220;
if(maxval < PP221)
maxval = PP221;
if(maxval < PP222)
maxval = PP222;
PP000 -= maxval;
PP001 -= maxval;
PP002 -= maxval;
PP010 -= maxval;
PP011 -= maxval;
PP012 -= maxval;
PP020 -= maxval;
PP021 -= maxval;
PP022 -= maxval;
PP100 -= maxval;
PP101 -= maxval;
PP102 -= maxval;
PP110 -= maxval;
PP111 -= maxval;
PP112 -= maxval;
PP120 -= maxval;
PP121 -= maxval;
PP122 -= maxval;
PP200 -= maxval;
PP201 -= maxval;
PP202 -= maxval;
PP210 -= maxval;
PP211 -= maxval;
PP212 -= maxval;
PP220 -= maxval;
PP221 -= maxval;
PP222 -= maxval;
double num( exp(PP001) );
double den(0);
den += exp(PP000);
den += exp(PP001);
den += exp(PP002);
den += exp(PP010);
den += exp(PP011);
den += exp(PP012);
den += exp(PP020);
den += exp(PP021);
den += exp(PP022);
den += exp(PP100);
den += exp(PP101);
den += exp(PP102);
den += exp(PP110);
den += exp(PP111);
den += exp(PP112);
den += exp(PP120);
den += exp(PP121);
den += exp(PP122);
den += exp(PP200);
den += exp(PP201);
den += exp(PP202);
den += exp(PP210);
den += exp(PP211);
den += exp(PP212);
den += exp(PP220);
den += exp(PP221);
den += exp(PP222);
return (num/den);
}
//////////////////
struct caller {
char set_by; // -1 when initialized or reset, 0 when set by GPU computation, 1 when set by CPU computation.
thrust::host_vector<double> call_probty;
thrust::device_vector<double> device_call_probty;
caller(const sample_info &);
void reset();
void worker (const AD_info & ADIO, const EM_worker & EMWO, const sample_info & SIO, const conditional_probty_table & CPTO);
void worker_CPU(const AD_info & ADIO, const EM_worker & EMWO, const sample_info & SIO, const conditional_probty_table & CPTO);
private:
double worker_CPU_aux(const std::vector<std::vector<int> > &, const EM_worker &, const conditional_probty_table &);
};
void caller::reset() {
for(size_t i(0);i<call_probty.size();++i)
call_probty[i] = 0;
thrust::copy(call_probty.begin(), call_probty.end(), device_call_probty.begin());
set_by = -1;
}
std::ostream & operator << (std::ostream & out, const caller & O) {
using namespace std;
out << "caller:\n";
out << "*******\n";
if(O.set_by == -1) {
out<< "initialized or reset\n";
out<< "--------------------\n";
}
else
if(O.set_by == 0) {
out<< "set by GPU\n";
out<< "----------\n";
}
else
if(O.set_by == 1) {
out<< "set by CPU\n";
out<< "----------\n";
}
else
throw(domain_error("ERROR in displaying caller"));
out << "call_probty:\n";
out << O.call_probty <<"\t"<< ":length = " << O.call_probty.size() <<"\n";
out << "device_call_probty:\n";
out << O.device_call_probty <<"\t"<< ":length = "<< O.device_call_probty.size() <<"\n";
return out;
}
caller::caller(const sample_info & SIO) {
call_probty = thrust::host_vector<double>( SIO.trios.size() );
device_call_probty = thrust::device_vector<double>( SIO.trios.size() );
set_by = -1;
}
void caller::worker(const AD_info & ADIO, const EM_worker & EMWO, const sample_info & SIO, const conditional_probty_table & CPTO) {
typedef thrust::device_vector<int>::const_iterator map_iter;
typedef thrust::device_vector<int>::const_iterator source_iter;
typedef thrust::permutation_iterator<source_iter, map_iter> perm_iter;
perm_iter P1_beg0 ( ADIO.DAD0.begin() , SIO.device_P1_index.begin() );
perm_iter P1_beg1 ( ADIO.DAD1.begin() , SIO.device_P1_index.begin() );
perm_iter P1_ender0 ( ADIO.DAD0.end() , SIO.device_P1_index.end() );
perm_iter P1_ender1 ( ADIO.DAD1.end() , SIO.device_P1_index.end() );
perm_iter P2_beg0 ( ADIO.DAD0.begin() , SIO.device_P2_index.begin() );
perm_iter P2_beg1 ( ADIO.DAD1.begin() , SIO.device_P2_index.begin() );
perm_iter P2_ender0 ( ADIO.DAD0.end() , SIO.device_P2_index.end() );
perm_iter P2_ender1 ( ADIO.DAD1.end() , SIO.device_P2_index.end() );
perm_iter child_beg0 ( ADIO.DAD0.begin(), SIO.device_child_index.begin() );
perm_iter child_beg1 ( ADIO.DAD1.begin(), SIO.device_child_index.begin() );
perm_iter child_ender0 ( ADIO.DAD0.end() , SIO.device_child_index.end() );
perm_iter child_ender1 ( ADIO.DAD1.end() , SIO.device_child_index.end() );
typedef thrust::tuple<perm_iter, perm_iter, perm_iter, perm_iter, perm_iter, perm_iter> iter_tuple;
typedef thrust::zip_iterator<iter_tuple> zip_iter;
zip_iter zip_beg ( thrust::make_zip_iterator( thrust::make_tuple(P1_beg0 , P1_beg1 , P2_beg0 , P2_beg1 , child_beg0 , child_beg1 ) ) );
zip_iter zip_ender( thrust::make_zip_iterator( thrust::make_tuple(P1_ender0, P1_ender1, P2_ender0, P2_ender1, child_ender0, child_ender1) ) );
caller_unary_op CUOO(CPTO, EMWO.rho, EMWO.F);
thrust::transform(zip_beg, zip_ender, device_call_probty.begin(), CUOO);
thrust::copy(device_call_probty.begin(), device_call_probty.end(), call_probty.begin());
set_by = 0;
}
double caller::worker_CPU_aux(const std::vector<std::vector<int> > & trio_ADs, const EM_worker & EMWO, const conditional_probty_table & CPTO) {
using namespace std;
const double rho( EMWO.rho);
const vector<double> F( EMWO.F );
vector<vector<double> > LLs(3, vector<double>(3));
for(int i(0);i<3;++i) {
vector<double> & row( LLs[i] );
const vector<int> & AD( trio_ADs[i] );
if(AD.size() != 2)
throw(domain_error("ERROR in worker_CPU_aux"));
row[0] = AD[0]*log(rho) + AD[1]*log(1.0 - rho);
row[1] = -(AD[0] + AD[1])*LOG_2;
row[2] = AD[1]*log(rho) + AD[0]*log(1.0 - rho);
}
vector<double> combined(27);
for(int i(0);i<3;++i) {
for(int j(0);j<3;++j) {
for(int k(0);k<3;++k) {
const int I(9*i + 3*j + k);
combined[I] = CPTO.LOG_CPT[I] + LLs[0][i] + LLs[1][j] + LLs[2][k];
}
}
}