void setPrefixAndRegisterAsTemp(std::string const & prefix, uint64_t const numbwt, uint64_t const numgt)
{
setPrefix(prefix, numbwt, numgt);
for ( uint64_t i = 0; i < getGT().size(); ++i )
::libmaus2::util::TempFileRemovalContainer::addTempFile(getGT()[i]);
for ( uint64_t i = 0; i < getBWT().size(); ++i )
::libmaus2::util::TempFileRemovalContainer::addTempFile(getBWT()[i]);
::libmaus2::util::TempFileRemovalContainer::addTempFile(getHWT());
::libmaus2::util::TempFileRemovalContainer::addTempFile(getHist());
::libmaus2::util::TempFileRemovalContainer::addTempFile(getSampledISA());
}
void build(const char *textFileName) {
this->free();
unsigned char *text = readText(textFileName, this->textLen, (DATATYPE)0);
checkNullChar(text, this->textLen);
DATATYPE bwtLen;
unsigned char *bwt = getBWT(textFileName, text, this->textLen, bwtLen, (DATATYPE)0);
cout << "Huffman encoding ... " << flush;
encodeHuffFromText(2, bwt, bwtLen, this->code, this->codeLen);
cout << "Done" << endl;
cout << "Building WT ... " << flush;
this->wt->createHWT(bwt, bwtLen, this->code, this->codeLen);
delete[] bwt;
cout << "Done" << endl;
fillArrayC(text, this->textLen, this->c);
delete[] text;
cout << "Index successfully built" << endl;
}
