void Consolidator::findTruePctErrors( ErrorCalculator &e_obj,int ma_snp_ends, bool holdOut,int window,float ma_threshold, float empirical_ma_threshold )
{
for(int i=0;i<person_count;i++)
{
for(int j=i;j<person_count;j++)
{
for(int l=0;l<m_trueMatches[i][j].size();l++)
{
if(m_trueMatches[i][j][l].end==-1)
{
continue;
}
//handle moving averages calculation
//
int t1 = m_trueMatches[ i ][ j ][ l ].start +
( m_trueMatches[ i ][ j ][ l ].end -
m_trueMatches[ i ][ j ][ l ].start ) * 0.25;
int t2 = m_trueMatches[ i ][ j ][ l ].end -
( m_trueMatches[ i ][ j ][ l ].end -
m_trueMatches[ i ][ j ][ l ].start ) * 0.25;
//now we have the positions of the first and last 25% of the truly ibd SH
//all that's left to do is to pass them into the moving averages function, and obtain the max ma
//then store that in a vector, sort them, and find the xth percentile of that vector. That will be
//the ma that we use later
//for that "finalErrors" parameters, need to get the number of errors along the truly IBD SH first...
vector<vector<int> > trueErrors=e_obj.checkErrors( i, j, t1, t2);
vector<int>finalTrueErrors=e_obj.getFinalErrors( trueErrors );
//handles MA calculations
std::vector<float> av;
float current_max;
if(empirical_ma_threshold < 0.0){
av = e_obj.getTrueMovingAverages(finalTrueErrors,t1,t2,window);
current_max = av[0];
for(int q = 1; q < av.size(); q++){
if(av[q] > current_max){
current_max = av[q];
}
}
e_obj.addMaxAverage(current_max);
}
//
int temp1 = m_trueMatches[ i ][ j ][ l ].start +
( m_trueMatches[ i ][ j ][ l ].end -
m_trueMatches[ i ][ j ][ l ].start ) * 0.15; //Should probably stop doing this
int temp2 = m_trueMatches[ i ][ j ][ l ].end -
( m_trueMatches[ i ][ j ][ l ].end -
m_trueMatches[ i ][ j ][ l ].start ) * 0.15;
int start =0, end =0, fend = ( temp2 -temp1 ) ;
//since we are using MOL at this point, this will pick out a random SH from the set of non-truly IBD SH
//and use that length to define the region over which we find PIE. Unless you are changing something with MOL,
//don't ever read this next block
int randPers1, randPers2, pos;
randPers1 = std::rand() % person_count;
randPers2 = std::rand() % person_count;
if( randPers1 > randPers2 )
{
randPers1 = randPers1 + randPers2;
randPers2 = randPers1 - randPers2;
randPers1 = randPers1 - randPers2;
}
while( m_matches[ randPers1 ][ randPers2 ].size() <= 0 )
{
randPers1 = std::rand() % person_count;
randPers2 = std::rand() % person_count;
if( randPers1 > randPers2 )
{
randPers1 = randPers1 + randPers2;
randPers2 = randPers1 - randPers2;
randPers1 = randPers1 - randPers2;
}
}
pos = std::rand() % m_matches[ randPers1 ][ randPers2 ].size();
int len = m_matches[ randPers1 ][ randPers2 ][ pos ].end
- m_matches[ randPers1 ][ randPers2 ][ pos ].start;
if( len >= fend || len <= 0)
{
continue;
}
temp1 = temp1;
temp2 = temp1 + len;
//end crazy MOL stuff
vector<vector<int> > errors=e_obj.checkErrors( i, j, temp1, temp2);
vector<int>finalErrors=e_obj.getFinalErrors( errors );
float per_err = e_obj.getThreshold(finalErrors,temp1,temp2);//overload
m_errors.push_back( per_err );
if( holdOut )
{
float oppHom = ( e_obj.getOppHomThreshold( i, j, temp1, temp2 ) ) / ( temp2 -temp1 );
m_holdOutErrors.push_back( oppHom );
}
}
}
}
vector<float>maxes;
float cutoff = empirical_ma_threshold;
if(empirical_ma_threshold < 0.0){
maxes = e_obj.getMaxAverages();
std::sort(maxes.begin(),maxes.end());
e_obj.setMaxAverage(maxes);
cutoff = e_obj.getXthPercentile(ma_threshold);
}
e_obj.setCutoff(cutoff);//set the actual threshold to be used when calculating MA in all other SH
//
std::sort( m_errors.begin(), m_errors.end() );
std::sort( m_holdOutErrors.begin(), m_holdOutErrors.end() );
std::string str = " \n No of elements in error check are: "
+ NumberToString( m_errors.size() );
str = str + " \n No of elements in hold error check are: "
+ NumberToString( m_holdOutErrors.size() );
e_obj.log( str );
}
void Consolidator::findTrueSimplePctErrors( ErrorCalculator &e_obj, float PIElength, bool holdOut,int window, float ma_threshold, float empirical_ma_threshold )
{
for(int i=0;i<person_count;i++)
{
for(int j=i;j<person_count;j++)
{
for(int l=0;l<m_trueMatches[i][j].size();l++)
{
if(m_trueMatches[i][j][l].end==-1)
{
continue;
}
//-------------------------------------------------------------------------------------------------
int t1 = m_trueMatches[ i ][ j ][ l ].start +
( m_trueMatches[ i ][ j ][ l ].end -
m_trueMatches[ i ][ j ][ l ].start ) * 0.25;
int t2 = m_trueMatches[ i ][ j ][ l ].end -
( m_trueMatches[ i ][ j ][ l ].end -
m_trueMatches[ i ][ j ][ l ].start ) * 0.25;
/*What do these two functions do? Is this necessary for being able to find errors, or
is it only useful for MA calculations?*/
vector<vector<int> > trueErrors=e_obj.checkErrors( i, j, t1, t2);
vector<int>finalTrueErrors=e_obj.getFinalErrors( trueErrors );
/*x*/
//This section handles finding the maximum moving averages amongst trulyIBD segments
std::vector<float> av;
float current_max;
if(empirical_ma_threshold < 0.0){
av = e_obj.getTrueMovingAverages(finalTrueErrors,t1,t2,window);
current_max = av[0];
for(int q = 1; q < av.size(); q++){
if(av[q] > current_max){
current_max = av[q];
}
}
e_obj.addMaxAverage(current_max);
}
//------------------------------------------------------------------------------
int temp1 = m_trueMatches[i][j][l].start;
int temp2 = m_trueMatches[i][j][l].end;
float startCM = e_obj.getCMDistance( temp1 );
float endCM = e_obj.getCMDistance( temp2 );
float mid1CM = startCM + ( endCM - startCM ) / 2 - PIElength / 2;
float mid2CM = startCM + ( endCM - startCM ) / 2 + PIElength / 2;
while( e_obj.getCMDistance( temp1 ) <= mid1CM || e_obj.getCMDistance( temp2 ) >=mid2CM )
{
if( e_obj.getCMDistance( temp1 ) <= mid1CM )
{
++temp1;
}
if( e_obj.getCMDistance( temp2 ) >=mid2CM )
{
--temp2;
}
}
/*Here they are again.
*/
vector<vector<int> > errors=e_obj.checkErrors( i, j, temp1, temp2);
vector<int>finalErrors=e_obj.getFinalErrors( errors );
// float per_err = e_obj.getThreshold(finalErrors,temp1, temp2, 0 );
float per_err = e_obj.getThreshold(finalErrors,temp1,temp2); //overload!
m_errors.push_back( per_err );
/*x*/
}//end for(l)
}//end for(j)
}//end for(i)
//this section actually handles the sorting of the max averages, and the setting of the user supplied percentile.
vector<float>maxes;
float cutoff = empirical_ma_threshold; //assume the user wanted to supply a value. This value will be overwritten shortly if they did not.
if(empirical_ma_threshold < 0.0){
maxes = e_obj.getMaxAverages();
std::sort(maxes.begin(),maxes.end());
e_obj.setMaxAverage(maxes);
cutoff = e_obj.getXthPercentile(ma_threshold); //<-make that an actual user input value
}
e_obj.setCutoff(cutoff);//set the actual threshold to be used when calculating MA in all other SH
if(empirical_ma_threshold < 0.0){
ma_thresh_str = "User supplied ma-threshold is: " + NumberToString(ma_threshold);
emp_ma_thresh_str = "Moving Averages will be tested usign the empirical threshold: " + NumberToString(cutoff);
} else {
emp_ma_thresh_str = "Moving Averages will be tested usign the empirical threshold: " + NumberToString(cutoff);
}
//----------------------------------------
std::sort( m_errors.begin(), m_errors.end() );
std::sort( m_holdOutErrors.begin(), m_holdOutErrors.end() );
ibg_str = "No of segments deemed to be IBD for finding empirical error threshold "
+ NumberToString( m_errors.size() );
}//end ftspe