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fix gcc9 compatibility issue
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Rongfeng Cui authored and Rongfeng Cui committed Mar 17, 2021
1 parent c2e3e2d commit 9a93aac
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4 changes: 4 additions & 0 deletions Population.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -714,6 +714,8 @@ bool Population::ImmigrateConfirm(bool bForceExistingDie) {
}
}
}

return ((nAddedMales+nAddedFemales)>0);
}

int Population::GetPopSize(int nMode) {
Expand All @@ -725,6 +727,8 @@ int Population::GetPopSize(int nMode) {
case 4: return _mpFemales.size()+_mpMales.size();
case 5: {int nCount=0; for( int nCpu=0;nCpu<nTotalCPUCore;nCpu++) {nCount+=_mpvNewGenMales[nCpu].size()+ _mpvNewGenFemales[nCpu].size();} return nCount;};
}

return 0;
}

void Population::Sample(ofstream &fMarkerOutFile, ofstream &fGeneOutFile, ofstream &fPhenotypeOutFile, ofstream &fPhenoSumOutFile, ofstream &fOffSpringNatSelProb ) {
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Binary file added bin/admixemp
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24 changes: 24 additions & 0 deletions bin/downsample_genotype.php
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@@ -0,0 +1,24 @@
<?php

$fIn1 = fopen("genotypes.txt", "r");
$fOut1 = fopen("genotypes.2.txt","w");
$fIn2 = fopen("outcomevars.txt", "r");
$fOut2 = fopen("outcomevars.2.txt","w");

for($i=0;$i<=2000;$i++) {

$sLn1 = fgets($fIn1);
$sLn2 = fgets($fIn2);
if ($i<=500 || $i>=1500) {
if ($sLn1 !=false ) {
fwrite($fOut1 , $sLn1 );
}

if ($sLn2!=false ) {
fwrite($fOut2 , $sLn2);
}

}
}

?>
331 changes: 331 additions & 0 deletions bin/export_genotype.php
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@@ -0,0 +1,331 @@
<?php
$sGenotypeFile = "";
$sExportPath = "";
$sMarkerSubsetFile = "";
$nPop1=0;
$nPop2=0;
$nPop3=0;

while(count($argv) > 0) {
$arg = array_shift($argv);
switch($arg) {
case '-s':
$sGenotypeFile = array_shift($argv);
break;
case '-o':
$sExportPath = array_shift($argv);
break;
case '-i':
$sMarkerSubsetFile = array_shift($argv);
break;
case '-pop1':
$nPop1 = array_shift($argv);
break;
case '-pop2':
$nPop2 = array_shift($argv);
break;
case '-pop3':
$nPop3 = array_shift($argv);
break;
}
}

/* print them */
echo("This is php. $sGenotypeFile, $sExportPath, $sMarkerSubsetFile.\n");

//read marker subset file:
$fMarkerSubsetFile = fopen($sMarkerSubsetFile, "r");
$arrMarkersToSample = array();

while(($sLn = fgets( $fMarkerSubsetFile ))!==false) {
//echo($sLn);
$arrCols = explode("\t", $sLn);
$nChr = $arrCols[0];
$nIndex = $arrCols[1];
if (!isset($arrMarkersToSample[$nChr])) {
$arrMarkersToSample[$nChr] = array();
}

array_push( $arrMarkersToSample[$nChr] , intval($nIndex));

}
fclose($fMarkerSubsetFile );

$sPriorAlleleFreqFile = "$sExportPath/priorallelefreqs.txt";
$sExGenotypesFile = "$sExportPath/genotypes.txt";

$fGenotypeFile = fopen($sGenotypeFile , "r"); // source

$fPriorAlleleFreqFile = fopen($sPriorAlleleFreqFile , "w");
$fExGenotypesFile = fopen($sExGenotypesFile , "w");

$sLn = "";
$bHeaderWritten = false;

if ($fGenotypeFile == false ) {
echo("Input file not found\n");
}


$arrAlleleCount_bigA_Pop1 = array();
$arrAlleleCount_bigA_Pop2 = array();
$arrAlleleCount_littleA_Pop1 = array();
$arrAlleleCount_littleA_Pop2 = array();
$arrAlleleName = array();
$arrAlleleTemp = array();
$nChrSide=0;



//print(count($arrMarkersToSample[1]));
//die();
// die();
$nCurrPop1=0;
$nCurrPop2=0;
$nCurrPop3=0;

$nLnCount = -1;
$bFirstPop3 = true;

while(($sLn = fgets( $fGenotypeFile ))!==false) {
$nLnCount++;
$arrColumns = explode("\t", $sLn, 5);
//echo("lINE:".$nLnCount.PHP_EOL);

$nIndId = $arrColumns[0];
$nPopId = $arrColumns[1];
$nSex = $arrColumns[2];


//echo($arrColumns[0].PHP_EOL);
$nMarkersToSampleCount = 0;

if ($nPopId == 3 && $nLnCount ==0) {
die("ERROR: no samples are present for the parental populations. This is required for exporting to admixmap. Rerun your simulations with parental populations!");
}

if ($nPopId != 3) { // parental populations, used for calculating prior allele freq.
if ($nPopId == 1) {
$nCurrPop1++;
if ($nCurrPop1>$nPop1) {
continue;
}
}
if ($nPopId == 2) {
$nCurrPop2++;
if ($nCurrPop2>$nPop2) {
continue;
}
}

$arrColumns = array_slice(explode("\t", $sLn) , 5, -1);


$nCurrChr = 0;
$nCurrLocusOnChr = 0;
$nTotalLocus = 0;
//echo("$nPopId, $nIndId\n");

$nTotalCol = count($arrColumns);
//echo($nTotalCol.PHP_EOL);
for( $nCol = 0; $nCol < $nTotalCol; $nCol ++ )
{
//echo $nTempCounter.PHP_EOL;
$nCell = $arrColumns[$nCol];

if ($nCell == -1) {
$nCurrChr++;
$nCurrLocusOnChr = 1;
$nMarkersToSampleCount =0;
continue;
}
else {

//echo($nLnCount);
//die();
//echo($arrMarkersToSample[$nCurrChr-1][$nMarkersToSampleCount]."\t".$nCurrLocusOnChr.PHP_EOL);
if ($arrMarkersToSample[$nCurrChr-1][$nMarkersToSampleCount] != ($nCurrLocusOnChr - 1)) { //dont sample this locus
$nCurrLocusOnChr++;
//echo("exclude\n");
continue;
}


//echo("sample\n");

if ($nLnCount == 0) {
$arrAlleleCount_bigA_Pop1[$nTotalLocus] = 0;
$arrAlleleCount_bigA_Pop2[$nTotalLocus] = 0;
$arrAlleleCount_littleA_Pop1[$nTotalLocus] = 0;
$arrAlleleCount_littleA_Pop2[$nTotalLocus] = 0;
$arrAlleleName[$nTotalLocus] = "chr".$nCurrChr."_".$nCurrLocusOnChr;
//echo("line 0");
//die();
}


$nMarkersToSampleCount++;

$sAllele = substr($nCell , 0, 1);
//echo $sAllele.PHP_EOL;
if ($sAllele == "A") {


if ($nPopId == 1) {
//echo "la1".PHP_EOL;
$arrAlleleCount_bigA_Pop1[$nTotalLocus]++;//isset($arrAlleleCount_bigA_Pop1[$nTotalLocus])? ($arrAlleleCount_bigA_Pop1[$nTotalLocus] + 1) : 0;
}
if ($nPopId == 2) {
//echo "la2".PHP_EOL;
$arrAlleleCount_bigA_Pop2[$nTotalLocus]++;//= isset($arrAlleleCount_bigA_Pop2[$nTotalLocus])? ($arrAlleleCount_bigA_Pop2[$nTotalLocus] + 1) : 0;
}
}

if ($sAllele == "a") {
if ($nPopId == 1) {
//echo "la3".PHP_EOL;
$arrAlleleCount_littleA_Pop1[$nTotalLocus]++ ;// = isset($arrAlleleCount_littleA_Pop1[$nTotalLocus])? ($arrAlleleCount_littleA_Pop1[$nTotalLocus] + 1) : 0;
}
if ($nPopId == 2) {
//echo "la4".PHP_EOL;
$arrAlleleCount_littleA_Pop2[$nTotalLocus]++ ;// = isset($arrAlleleCount_littleA_Pop2[$nTotalLocus])? ($arrAlleleCount_littleA_Pop2[$nTotalLocus] + 1) : 0;
}
}
/*
if ( $nLnCount == 0)
{
$arrAlleleName[$nTotalLocus] = "chr".$nCurrChr."_".$nCurrLocusOnChr;
print_r($arrAlleleName);
die();
}
else {
print_r($arrAlleleName);
die();
}
*/

$nTotalLocus++;
$nCurrLocusOnChr++;


}
}
}

else {
$nCurrPop3++;

if ($nCurrPop3 > $nPop3) {
continue;
}
$arrColumns = array_slice(explode("\t", $sLn) , 5, -1);

//echo($nTotalLocus.PHP_EOL);
$nCurrChr = 0;
$nCurrLocusOnChr = 0;
$nTotalLocus = 0;
$nTotalMarkers = count($arrAlleleName);

if ($bFirstPop3) { // write genotypes.txt header


fwrite( $fExGenotypesFile , "id\t");
//echo($nTotalMarkers);
//die();
for ($nMarker=0;$nMarker< $nTotalMarkers ;$nMarker++) {
fwrite( $fExGenotypesFile , $arrAlleleName[$nMarker]);
if ($nMarker != $nTotalMarkers-1) {
fwrite( $fExGenotypesFile , "\t");
}
}
//fwrite( $fExGenotypesFile , PHP_EOL);
$bFirstPop3=false;
}

//echo("$nPopId, $nIndId\n");
$nTotalCol = count($arrColumns);
if ($nChrSide == 1)
{
fwrite( $fExGenotypesFile , PHP_EOL."$nIndId\t");
}
//echo($nTotalCol.PHP_EOL);
for( $nCol = 0; $nCol < $nTotalCol; $nCol++ )
{
//echo $nTempCounter.PHP_EOL;
$nCell = $arrColumns[$nCol];

if ($nCell == "-1") {
//echo("col$nCol\n" );
$nCurrChr++;
$nCurrLocusOnChr = 1;
$nMarkersToSampleCount =0;
continue;
}
else {
/*
if($nMarkersToSampleCount == 446 && $nCurrChr==1) {
echo("chr1 sucess");
die();
}
echo($nMarkersToSampleCount."\t".($arrMarkersToSample[$nCurrChr-1][$nMarkersToSampleCount])."\t".($nCurrLocusOnChr-1).PHP_EOL);
if ($nCurrChr > 1) {
die();
}
*/
if ($arrMarkersToSample[$nCurrChr-1][$nMarkersToSampleCount] != ($nCurrLocusOnChr-1)) { //dont sample this locus
$nCurrLocusOnChr++;

continue;
}

$nMarkersToSampleCount++;

$sAllele = substr($nCell , 0, 1);
//echo $sAllele.PHP_EOL;
if ($nChrSide == 0) {
$arrAlleleTemp[$nTotalLocus] = ($sAllele=="A")? 1:2;//save this to temp array;
}
else {
/*
echo(count($arrAlleleTemp).PHP_EOL);
die();
*/
fwrite( $fExGenotypesFile , "\"".$arrAlleleTemp[$nTotalLocus].",".(($sAllele=="A")? 1:2)."\"");

//echo($nMarkersToSampleCount.PHP_EOL);

if ($nMarkersToSampleCount != $nTotalMarkers-1) {
fwrite( $fExGenotypesFile , "\t");

}

}
$nCurrLocusOnChr++;
$nTotalLocus++;
}
}



}

$nChrSide = ($nChrSide==0)? 1:0;

}

//write priorallelefreq file:
$nTotalMarkers = count($arrAlleleName);
echo("Writing priorallelefreq...\n");
fwrite( $fPriorAlleleFreqFile , "LocusNames\tPop1\tPop2".PHP_EOL);
for ($nMarker=0;$nMarker< $nTotalMarkers ;$nMarker++) {
fwrite( $fPriorAlleleFreqFile , $arrAlleleName[$nMarker]."\t".($arrAlleleCount_bigA_Pop1[$nMarker]+0.5)."\t".($arrAlleleCount_bigA_Pop2[$nMarker]+0.5).PHP_EOL);
fwrite( $fPriorAlleleFreqFile , $arrAlleleName[$nMarker]."\t".($arrAlleleCount_littleA_Pop1[$nMarker]+0.5)."\t".($arrAlleleCount_littleA_Pop2[$nMarker]+0.5).PHP_EOL);
}

fclose($fGenotypeFile);
fclose($fPriorAlleleFreqFile);
fclose($fExGenotypesFile);

?>
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