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filter by frequency of heterozygote genotypes #294

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merged 4 commits into from
May 18, 2020
Merged

filter by frequency of heterozygote genotypes #294

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a34a006
max heterozygote filter
nspope Mar 15, 2020
6786964
heterozygote freq filter works
nspope Mar 15, 2020
8ec13ae
added minHetFreq
nspope Mar 15, 2020
26d7057
Merge branch 'master' into hetFilter
nspope May 18, 2020
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32 changes: 27 additions & 5 deletions abcHWE.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,8 @@ void abcHWE::printArg(FILE *argFile){
fprintf(argFile,"\t-doHWE\t%d\n",doHWE);
fprintf(argFile,"\t-minHWEpval\t%f\n",minHWEpval);
fprintf(argFile,"\t-maxHWEpval\t%f\n",maxHWEpval);
fprintf(argFile,"\t-maxHetFreq\t%f\n",maxHetFreq);//nspope;hetFilter
fprintf(argFile,"\t-minHetFreq\t%f\n",minHetFreq);//nspope;hetFilter
fprintf(argFile,"\n");
}

Expand All @@ -37,6 +39,8 @@ void abcHWE::getOptions(argStruct *arguments){

minHWEpval = angsd::getArg("-minHWEpval",minHWEpval,arguments);
maxHWEpval = angsd::getArg("-maxHWEpval",maxHWEpval,arguments);
maxHetFreq = angsd::getArg("-maxHetFreq",maxHetFreq,arguments);//nspope;hetFilter
minHetFreq = angsd::getArg("-minHetFreq",minHetFreq,arguments);//nspope;hetFilter


if(arguments->inputtype==INPUT_BEAGLE||arguments->inputtype==INPUT_VCF_GP){
Expand All @@ -55,6 +59,8 @@ abcHWE::abcHWE(const char *outfiles,argStruct *arguments,int inputtype){
doHWE = 0;
maxHWEpval = -1;
minHWEpval = -1;
maxHetFreq = -1;//nspope;hetFilter
minHetFreq = -1;//nspope;hetFilter
testMe=0;
tolStop = 0.00001;
bufstr.s=NULL;bufstr.l=bufstr.m=0;
Expand All @@ -77,8 +83,14 @@ abcHWE::abcHWE(const char *outfiles,argStruct *arguments,int inputtype){
outfileZ = aio::openFileBG(outfiles,postfix);

//print header
const char *str = "Chromo\tPosition\tMajor\tMinor\thweFreq\tFreq\tF\tLRT\tp-value\n";
aio::bgzf_write(outfileZ,str,strlen(str));
if (maxHetFreq != -1 || minHetFreq != -1) //nspope;maxHetFilter
{
const char *str = "Chromo\tPosition\tMajor\tMinor\thweFreq\tFreq\tF\tLRT\tp-value\thetFreq\n";
aio::bgzf_write(outfileZ,str,strlen(str));
} else {
const char *str = "Chromo\tPosition\tMajor\tMinor\thweFreq\tFreq\tF\tLRT\tp-value\n";
aio::bgzf_write(outfileZ,str,strlen(str));
}

}

Expand All @@ -98,6 +110,7 @@ void abcHWE::clean(funkyPars *pars){
funkyHWE *hweStruct =(funkyHWE *) pars->extras[index];
delete[] hweStruct->freq;
delete[] hweStruct->freqHWE;
delete[] hweStruct->hetfreq;//nspope;hetFilter
delete[] hweStruct->F;
delete[] hweStruct->like0;
delete[] hweStruct->pval;
Expand All @@ -118,7 +131,11 @@ void abcHWE::print(funkyPars *pars){

float lrt= 2*hweStruct->like0[s]-2*hweStruct->likeF[s];

ksprintf(&bufstr,"%s\t%d\t%c\t%c\t%f\t%f\t%f\t%e\t%e\n",header->target_name[pars->refId],pars->posi[s]+1,intToRef[pars->major[s]],intToRef[pars->minor[s]],hweStruct->freqHWE[s],hweStruct->freq[s],hweStruct->F[s],lrt,hweStruct->pval[s]);
if (maxHetFreq!=-1 || minHetFreq!=-1){//nspope;hetFilter
ksprintf(&bufstr,"%s\t%d\t%c\t%c\t%f\t%f\t%f\t%e\t%e\t%f\n",header->target_name[pars->refId],pars->posi[s]+1,intToRef[pars->major[s]],intToRef[pars->minor[s]],hweStruct->freqHWE[s],hweStruct->freq[s],hweStruct->F[s],lrt,hweStruct->pval[s],hweStruct->hetfreq[s]);
} else {
ksprintf(&bufstr,"%s\t%d\t%c\t%c\t%f\t%f\t%f\t%e\t%e\n",header->target_name[pars->refId],pars->posi[s]+1,intToRef[pars->major[s]],intToRef[pars->minor[s]],hweStruct->freqHWE[s],hweStruct->freq[s],hweStruct->F[s],lrt,hweStruct->pval[s]);
}

}
aio::bgzf_write(outfileZ,bufstr.s,bufstr.l);bufstr.l=0;
Expand All @@ -134,6 +151,7 @@ void abcHWE::run(funkyPars *pars){

double *freq = new double[pars->numSites];
double *freqHWE = new double[pars->numSites];
double *hetfreq = new double[pars->numSites];//nspope;hetFilter
double *F = new double[pars->numSites];
double *like0 = new double[pars->numSites];
double *likeF = new double[pars->numSites];
Expand Down Expand Up @@ -188,15 +206,19 @@ void abcHWE::run(funkyPars *pars){

if(minHWEpval!=-1 && pval[s] < minHWEpval)
pars->keepSites[s] = 0;



//nspope;hetFilter
hetfreq[s] = 2.*(1.-x[1])*x[0]*(1.-x[0]);
if( (maxHetFreq!=-1 && hetfreq[s] > maxHetFreq) ||
(minHetFreq!=-1 && hetfreq[s] < minHetFreq) )
pars->keepSites[s] = 0;

}


hweStruct->freq=freq;
hweStruct->freqHWE=freqHWE;
hweStruct->hetfreq=hetfreq;//nspope;hetFilter
hweStruct->F=F;
hweStruct->like0=like0;
hweStruct->pval=pval;
Expand Down
4 changes: 4 additions & 0 deletions abcHWE.h
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,8 @@ typedef struct {
double *pval;

double *F;

double *hetfreq;//nspope;hetFilter
}funkyHWE;


Expand All @@ -26,6 +28,8 @@ class abcHWE:public abc{
int doHWE;
double minHWEpval;
double maxHWEpval;
double maxHetFreq;//nspope;hetFilter
double minHetFreq;//nspope;hetFilter
int testMe;
double tolStop;
double differ(double *x,double *y);
Expand Down