// Parse a BWT from a file
RLBWT::RLBWT(const std::string& filename, int sampleRate) : m_numStrings(0),
m_numSymbols(0),
m_largeSampleRate(DEFAULT_SAMPLE_RATE_LARGE),
m_smallSampleRate(sampleRate)
{
IBWTReader* pReader = BWTReader::createReader(filename);
pReader->read(this);
initializeFMIndex();
delete pReader;
}
// Construct the BWT from a suffix array
RLBWT::RLBWT(const SuffixArray* pSA, const ReadTable* pRT)
{
// Set up BWT state
size_t n = pSA->getSize();
m_smallSampleRate = DEFAULT_SAMPLE_RATE_SMALL;
m_largeSampleRate = DEFAULT_SAMPLE_RATE_LARGE;
m_numStrings = pSA->getNumStrings();
m_numSymbols = n;
RLUnit currRun;
// Set up the bwt string and suffix array from the cycled strings
for(size_t i = 0; i < n; ++i)
{
SAElem saElem = pSA->get(i);
const SeqItem& si = pRT->getRead(saElem.getID());
// Get the position of the start of the suffix
uint64_t f_pos = saElem.getPos();
uint64_t l_pos = (f_pos == 0) ? si.seq.length() : f_pos - 1;
char b = (l_pos == si.seq.length()) ? '$' : si.seq.get(l_pos);
// Add to the current run or append in the new char
if(currRun.isInitialized())
{
if(currRun.getChar() == b && !currRun.isFull())
{
currRun.incrementCount();
}
else
{
// Write out the old run and start a new one
assert(currRun.isInitialized());
m_rlString.push_back(currRun);
currRun = RLUnit(b);
}
}
else
{
// Start a new run
currRun = RLUnit(b);
}
}
assert(currRun.isInitialized());
if(currRun.isInitialized())
m_rlString.push_back(currRun);
initializeFMIndex();
}
// Construct the BWT from a suffix array
SBWT::SBWT(const SuffixArray* pSA, const ReadTable* pRT)
{
size_t n = pSA->getSize();
m_numStrings = pSA->getNumStrings();
m_bwStr.resize(n);
// Set up the bwt string and suffix array from the cycled strings
for(size_t i = 0; i < n; ++i)
{
SAElem saElem = pSA->get(i);
const SeqItem& si = pRT->getRead(saElem.getID());
// Get the position of the start of the suffix
uint64_t f_pos = saElem.getPos();
uint64_t l_pos = (f_pos == 0) ? si.seq.length() : f_pos - 1;
char b = (l_pos == si.seq.length()) ? '$' : si.seq.get(l_pos);
m_bwStr.set(i, b);
}
initializeFMIndex(DEFAULT_SAMPLE_RATE);
}
// Parse a BWT from a file
SBWT::SBWT(const std::string& filename, int sampleRate)
{
BWTReaderBinary reader(filename);
reader.read(this);
initializeFMIndex(sampleRate);
}
