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#include "genomeParametersWrite.h"
#include "streamFuns.h"
void genomeParametersWrite(string fileName, Parameters& P, string errorOut, Genome &mapGen)
{//write the genome information into the genomePar stream
ofstream & genomePar = ofstrOpen(fileName, errorOut, P);
genomePar << "### "<<P.commandLineFull <<"\n";
genomePar << "### GstrandBit "<< int(mapGen.GstrandBit) <<"\n";
genomePar << "versionGenome\t" << P.versionGenome <<"\n";
genomePar << "genomeType\t" << mapGen.pGe.gTypeString <<"\n";
genomePar << "genomeFastaFiles\t";
for (uint ii=0;ii<mapGen.pGe.gFastaFiles.size();ii++)
genomePar << mapGen.pGe.gFastaFiles.at(ii) << " ";
genomePar << "\n";
genomePar << "genomeSAindexNbases\t" << mapGen.pGe.gSAindexNbases << "\n";
genomePar << "genomeChrBinNbits\t" << mapGen.pGe.gChrBinNbits << "\n";
genomePar << "genomeSAsparseD\t" << mapGen.pGe.gSAsparseD <<"\n";
genomePar << "genomeTransformType\t" << mapGen.pGe.transform.typeString <<"\n";
genomePar << "genomeTransformVCF\t" << mapGen.pGe.transform.vcfFile <<"\n";
genomePar << "sjdbOverhang\t" << mapGen.sjdbOverhang <<"\n";
genomePar << "sjdbFileChrStartEnd\t";
for (uint ii=0;ii<mapGen.pGe.sjdbFileChrStartEnd.size();ii++)
genomePar<< mapGen.pGe.sjdbFileChrStartEnd.at(ii) << " ";
genomePar<<"\n";
genomePar << "sjdbGTFfile\t" << mapGen.pGe.sjdbGTFfile <<"\n";
genomePar << "sjdbGTFchrPrefix\t" << mapGen.pGe.sjdbGTFchrPrefix <<"\n";
genomePar << "sjdbGTFfeatureExon\t" << mapGen.pGe.sjdbGTFfeatureExon <<"\n";
genomePar << "sjdbGTFtagExonParentTranscript\t" << mapGen.pGe.sjdbGTFtagExonParentTranscript <<"\n";
genomePar << "sjdbGTFtagExonParentGene\t" << mapGen.pGe.sjdbGTFtagExonParentGene <<"\n";
genomePar << "sjdbInsertSave\t" << mapGen.pGe.sjdbInsertSave <<"\n";
genomePar << "genomeFileSizes\t" << mapGen.pGe.gFileSizes.at(0);
for (uint ii=1;ii<mapGen.pGe.gFileSizes.size();ii++)
genomePar << " " << mapGen.pGe.gFileSizes.at(ii) ;
genomePar << "\n";
genomePar.close();
};
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