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#include "Genome.h"
#include "SuffixArrayFuns.h"
#include "PackedArray.h"
#include "ErrorWarning.h"
#include "streamFuns.h"
void Genome::genomeOutLoad(){//allocate and load *output* Genome
Parameters P1;
ifstream parFile((pGe.gDir+("/genomeParameters.txt")).c_str());
if (parFile.good()) {
P.inOut->logMain << "Reading output genome generation parameters:\n";
P1.inOut = P.inOut;
P1.scanAllLines(parFile,3,-1);
parFile.close();
} else {
ostringstream errOut;
errOut << "EXITING because of FATAL ERROR: could not open genome file "<< pGe.gDir+("/genomeParameters.txt") << endl;
errOut << "SOLUTION: check that the path to genome files, specified in --genomeDir is correct and the files are present, and have user read permsissions\n" <<flush;
exitWithError(errOut.str(),std::cerr, P.inOut->logMain, EXIT_CODE_GENOME_FILES, P);
};
//find chr starts from files
chrInfoLoad();
ifstream GenomeIn;
nGenome = OpenStream("Genome", GenomeIn, 0);
G=new char[nGenome];
//uint64 genomeReadBytesN =
fstreamReadBig(GenomeIn,G,nGenome);
GenomeIn.close();
Genome::loadSJDB(pGe.gDir);
//record required genome parameters in P
pGe.gSAindexNbases=P1.pGe.gSAindexNbases;
pGe.gChrBinNbits=P1.pGe.gChrBinNbits;
genomeChrBinNbases=1LLU<<pGe.gChrBinNbits;
pGe.gSAsparseD=P1.pGe.gSAsparseD;
pGe.gType=1;
chrBinFill();
ifstream &convStream= ifstrOpen(genomeOut.convFile, ERROR_OUT, "SOLUTION: regenerate genome.", P);
uint32 nconv;
convStream >> nconv >> genomeOut.nMinusStrandOffset;
genomeOut.convBlocks.resize(nconv+1);
for (uint32 ii=0; ii<nconv; ii++)
convStream >> genomeOut.convBlocks[ii][0] >> genomeOut.convBlocks[ii][1] >> genomeOut.convBlocks[ii][2];
//genomeOut.convBlocks[nconv][0]=genomeOut.convBlocks[nconv-1][0]+genomeOut.convBlocks[nconv-1][1];
genomeOut.convBlocks[nconv-1][1] +=1;//increase the length of the last block so that we never reach the last base
genomeOut.convBlocks[nconv][0]=(uint64)-1;//start of the block after last is infinity
};
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