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#include "ParametersGenome.h"
#include "Parameters.h"
#include "ErrorWarning.h"
void ParametersGenome::initialize(Parameters *pPin)
{
pP=pPin;
if (gDir.back()!='/') {
gDir += '/';
};
//genome transformation
if (transform.typeString=="None") {
transform.type=0;
} else if (transform.typeString=="Haploid") {
transform.type=1;
} else if (transform.typeString=="Diploid") {
transform.type=2;
} else {
ostringstream errOut;
errOut << "EXITING because of FATAL PARAMETER ERROR: unrecognized option in --outTransformType = " << transform.typeString << "\n";
errOut << "SOLUTION: use one of the allowed values for --outTransformType : 'None' or 'Haploid' or 'Diploid' \n";
exitWithError(errOut.str(), std::cerr, pP->inOut->logMain, EXIT_CODE_PARAMETER, *pP);
};
transform.outYes = transform.outSAM = transform.outSJ = false;
if (transform.output.at(0) == "None") {
//nothing to do
} else {
for (auto &ot: transform.output) {
if (ot == "SAM") {
transform.outYes = transform.outSAM = true;
} else if (ot == "SJ") {
transform.outYes = transform.outSJ = true;
} else {
exitWithError("EXITING because of FATAL PARAMETER ERROR: unrecognized option in --outTransformOutput = " + ot + '\n'
+ "SOLUTION: use allowed values for --outTransformOutput: None or SAM and/or SJ\n"
,std::cerr, pP->inOut->logMain, EXIT_CODE_PARAMETER, *pP);
};
};
};
if (gTypeString!="Full" && gTypeString!="Transcriptome" && gTypeString!="SuperTranscriptome") {
ostringstream errOut;
errOut << "EXITING because of FATAL parameter error: --genomeType=" << gTypeString << "\n";
errOut << "SOLUTION: use one of the allowed values for --genomeLoad : Full OR Transcriptome OR SuperTranscriptome\n" <<flush;
exitWithError(errOut.str(),std::cerr, pP->inOut->logMain, EXIT_CODE_PARAMETER, *pP);
};
if (gLoad!="LoadAndKeep" && gLoad!="LoadAndRemove" && gLoad!="Remove" && gLoad!="LoadAndExit" && gLoad!="NoSharedMemory") {// find shared memory fragment
ostringstream errOut;
errOut << "EXITING because of FATAL INPUT ERROR: --genomeLoad=" << gLoad << "\n" <<flush;
errOut << "SOLUTION: use one of the allowed values for --genomeLoad : NoSharedMemory,LoadAndKeep,LoadAndRemove,LoadAndExit,Remove.\n" <<flush;
exitWithError(errOut.str(),std::cerr, pP->inOut->logMain, EXIT_CODE_PARAMETER, *pP);
};
};
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