msisensor/sample.cpp at master · ding-lab/msisensor · GitHub

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* sample.cpp for MSIsensor

* Permission is hereby granted, free of charge, to any person

* obtaining a copy of this software and associated documentation

* files (the "Software"), to deal in the Software without

* restriction, including without limitation the rights to use,

* copy, modify, merge, publish, distribute, sublicense, and/or sell

* copies of the Software, and to permit persons to whom the

* Software is furnished to do so, subject to the following

* conditions:

* The above copyright notice and this permission notice shall be

* included in all copies or substantial portions of the Software.

* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,

* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES

* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND

* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT

* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,

* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING

* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR

* OTHER DEALINGS IN THE SOFTWARE.

#include <iostream>

#include <sstream>

#include <bitset>

#include <omp.h>

#include <iomanip>

#include "sample.h"

#include "param.h"

extern Param paramd;

Sample::Sample()

: outputPrefix( "test" )

, output( NULL )

//, outputPSomatic( NULL )

, outputSomatic( NULL )

, outputGermline( NULL )

, outputDistribution( NULL )

, numberOfSites( 0 )

, precisionNumS( 2 )

, precisionNumL( 5 )

, numberOfDataPoints( 0 )

, numberOfMsiDataPoints( 0 )

, numberOftotalSites( 0 )

{

//xxxx

output.precision( precisionNumS );

// outputPSomatic.precision( precisionNumL );

outputSomatic.precision( precisionNumL );

outputGermline.precision( precisionNumL );

outputDistribution.precision( precisionNumL );

};

Sample::~Sample() {

// xxxxx

};

void Sample::iniOutput( const std::string &gavePrefix ) {

if ( !gavePrefix.empty() ) { outputPrefix = gavePrefix; }

// init pour out result files

output.open( outputPrefix.c_str() );

// outputPSomatic.open( (outputPrefix + "_p_somatic").c_str() );

outputSomatic.open( (outputPrefix + "_somatic").c_str() );

outputGermline.open( (outputPrefix + "_germline").c_str() );

outputDistribution.open( (outputPrefix + "_dis").c_str() );

//if ( !output || !outputPSomatic || !outputSomatic || !outputGermline || !outputDistribution ) {

if ( !output || !outputSomatic || !outputGermline || !outputDistribution ) {

std::cerr <<"failed to open output files to write !"<< std::endl;

exit(1);

}

void Sample::iniTumorDisOutput( const std::string &gavePrefix ) {

if ( !gavePrefix.empty() ) { outputPrefix = gavePrefix; }

// init pour out result files

output.open( outputPrefix.c_str() );

outputSomatic.open( (outputPrefix + "_somatic").c_str() );

outputDistribution.open( (outputPrefix + "_dis").c_str() );

//if ( !output || !outputPSomatic || !outputSomatic || !outputGermline || !outputDistribution ) {

if ( !output || !outputDistribution || !outputSomatic) {

std::cerr <<"failed to open output files to write !"<< std::endl;

exit(1);

}

void Sample::pourOutMsiScore() {

output << "Total_Number_of_Sites\tNumber_of_Somatic_Sites\t%" << std::endl;

if ( numberOfDataPoints != 0) {

output << numberOfDataPoints << "\t"

<< numberOfMsiDataPoints << "\t"

<< std::fixed

<< (numberOfMsiDataPoints / (double)numberOfDataPoints) * 100.0 << std::endl;

} else {

output << numberOfDataPoints << "\t"

<< numberOfMsiDataPoints << "\t"

<< std::setprecision(2)

<< std::fixed

<< 0.00 << std::endl;

}

void Sample::closeOutStream() {

output.close();

//outputPSomatic.close();

outputSomatic.close();

outputGermline.close();

outputDistribution.close();

}

// FDR determination

void Sample::calculateFDR() {

// sorting by p_value

sort( totalSomaticSites.begin(), totalSomaticSites.end() );

unsigned short rank = 1;

// FDR calculation

for ( std::vector< SomaticSite >::iterator _it = totalSomaticSites.begin(); _it != totalSomaticSites.end(); ++_it ) {

//_it->PourOut();

_it->FDR = _it->pValue * numberOfDataPoints / rank ;

if ( _it->FDR > paramd.fdrThreshold ) {

rank++;

continue;

} else {

_it->rank = rank;

_it->somatic = true;

numberOfMsiDataPoints++;

rank++;

}

// report somatics && FDR

void Sample::pourOutSomaticFDR() {

for ( std::vector< SomaticSite >::iterator _it = totalSomaticSites.begin(); _it != totalSomaticSites.end(); ++_it ) {

if ( ! _it->somatic ) continue;

outputSomatic << _it->chr << "\t"

<< _it->location << "\t"

<< _it->fbases << "\t"

<< _it->length << "\t"

<< _it->bases << "\t"

<< _it->ebases << "\t"

<< _it->diff << "\t"

<< _it->pValue << "\t"

<< _it->FDR << "\t"

<< _it->rank << "\n";

}

// verbose

void Sample::VerboseInfo() {

std::cerr << "\n*** Summary information ***\n\n"

<< "Number of total sites: "

<< numberOftotalSites << "\n"

<< "Number of sites with enough coverage: "

<< numberOfDataPoints << "\n"

<< "Number of MSI sites: "

<< numberOfMsiDataPoints << "\n";

}

msisensor/sample.cpp at master · ding-lab/msisensor · GitHub

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