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Return failure status for GL validation errors #664

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Return failure status for GL validation errors #664

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11 changes: 5 additions & 6 deletions abcCallGenotypes.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -69,23 +69,23 @@ void abcCallGenotypes::getOptions(argStruct *arguments){
doCounts = angsd::getArg("-doCounts",doCounts,arguments);
if((geno_minDepth!=-1 || geno_maxDepth!=-1 || geno_minMM!=-1 ) &&doCounts==0){
fprintf(stderr,"Must supply -doCounts to use a minimum depth for GC calling\n");
exit(0);
exit(EXIT_FAILURE);
}
if(geno_maxDepth!=-1&&doCounts==0){
fprintf(stderr,"Must supply -doCounts to use a maximum depth for GC calling\n");
exit(0);
exit(EXIT_FAILURE);
}


if(arguments->inputtype!=INPUT_BEAGLE&&doPost==0&&arguments->inputtype!=INPUT_VCF_GP){
fprintf(stderr,"\n\t-> You need -doPost to call genotypes \n");
exit(0);
exit(EXIT_FAILURE);

}

if(doPost==1&&doMaf==0){
fprintf(stderr,"\n\t-> You need -doMaf inorder to get posterior probabilities when using freq as prior\n");
exit(0);
exit(EXIT_FAILURE);
}
minInd=angsd::getArg("-minInd",minInd,arguments);

Expand All @@ -103,7 +103,7 @@ abcCallGenotypes::abcCallGenotypes(const char *outfiles,argStruct *arguments,int
if(arguments->argc==2){
if(!strcasecmp(arguments->argv[1],"-doGeno")){
printArg(stdout);
exit(0);
exit(EXIT_FAILURE);
}else
return;
}
Expand Down Expand Up @@ -280,4 +280,3 @@ void abcCallGenotypes::run(funkyPars *pars){

getGeno(pars);
}

20 changes: 10 additions & 10 deletions abcGL.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,7 @@ void readError(double **errors,const char *fname){
FILE *fp=NULL;
if(NULL==(fp=fopen(fname,"r"))){
fprintf(stderr,"Error opening file: %s\n",fname);
exit(0);
exit(EXIT_FAILURE);
}

char buf[LENS];
Expand Down Expand Up @@ -112,13 +112,13 @@ void abcGL::getOptions(argStruct *arguments){
doMajorMinor=angsd::getArg("-doMajorMinor",doMajorMinor,arguments);
if(GL!=0 && (arguments->inputtype==INPUT_GLF || arguments->inputtype==INPUT_GLF3 || arguments->inputtype==INPUT_VCF_GL)){
fprintf(stderr,"Can't calculate genotype likelihoods from -glf/-glf3/VCF files\n");
exit(0);
exit(EXIT_FAILURE);
}
if(arguments->inputtype==INPUT_GLF||arguments->inputtype==INPUT_GLF3||arguments->inputtype==INPUT_VCF_GL||arguments->inputtype==INPUT_GLF10_TEXT)
return;
if(doGlf&&GL==0){
fprintf(stderr,"\t-> You need to choose a genotype likelihood model -GL for dumping genotype likelihoods\n");
exit(0);
exit(EXIT_FAILURE);
}
if(GL==0&&doGlf==0){
shouldRun[index] =0;
Expand All @@ -133,15 +133,15 @@ void abcGL::getOptions(argStruct *arguments){

if(( GL<0||GL>7 )) {
fprintf(stderr,"\t-> You've choosen a GL model=%d, only 1,2,3,4,5,6,7 are implemented\n",GL);
exit(0);
exit(EXIT_FAILURE);
}
if(GL==4&&(doCounts==0)){
fprintf(stderr,"\t-> Must supply -doCounts 1 for SYK model\n");
exit(0);
exit(EXIT_FAILURE);
}
if(GL==6&&(doCounts==0)){
fprintf(stderr,"\t-> Must supply -doCounts 1 for -gl 6\n");
exit(0);
exit(EXIT_FAILURE);
}
/*
if(doGlf==2){
Expand All @@ -155,16 +155,16 @@ void abcGL::getOptions(argStruct *arguments){
*/
if((doGlf==2||doGlf==3) && doMajorMinor==0){
fprintf(stderr,"\t-> For dumping beaglestyle output you need to estimate major/minor: -doMajorMinor\n");
exit(0);
exit(EXIT_FAILURE);
}
if(arguments->inputtype==INPUT_BEAGLE&&doGlf){
fprintf(stderr,"\t-> cannot output likelihoods (doGlf) when input is beagle\n");
exit(0);
exit(EXIT_FAILURE);
}

if(arguments->inputtype!=INPUT_BAM&&arguments->inputtype!=INPUT_PILEUP){
fprintf(stderr,"Error: Likelihoods can only be estimated based on BAM input and uppile input\n");
exit(0);
exit(EXIT_FAILURE);
}


Expand Down Expand Up @@ -192,7 +192,7 @@ abcGL::abcGL(const char *outfiles,argStruct *arguments,int inputtype){
if(arguments->argc==2){
if(!strcasecmp(arguments->argv[1],"-GL")){
printArg(stdout);
exit(0);
exit(EXIT_FAILURE);
}else
return;
}
Expand Down