DNALength CompressedSequence<T_Sequence>::FourBitDecompressHomopolymers(int start, int end,
T_Sequence &decompSeq) {
decompSeq.Free(); // Free before decomp;
//
// first compute the length of the decoded
//
DNALength i;
decompSeq.length = 0;
for (i = start; i < end; i++ ){
unsigned char count;
count = (unsigned char) seq[i];
count >>= 4;
decompSeq.length += count;
}
decompSeq.seq = ProtectedNew<Nucleotide>(decompSeq.length);
//
// Now store the actual decompressed seq.
//
int d = 0;
unsigned char mask = 0xf;
for (i = start; i < end; i++ ){
unsigned char count;
count = (unsigned char) seq[i];
count >>= 4;
int j;
for (j = 0; j < count; j++ ){
decompSeq.seq[d] = FourBitToAscii[(seq[i] & mask)];
d++;
}
}
decompSeq.bitsPerNuc = 4;
decompSeq.deleteOnExit = true;
return decompSeq.length;
}
int GetNext(T_Sequence &ccsSequence) {
//
// Read in all ccs pass data.
//
ccsSequence.Free();
int retVal = 0;
if (this->curRead == ccsBasReader.nReads) {
return 0;
}
if (this->curBasePos == ccsBasReader.nBases) {
return 0;
}
try {
UInt numPasses;
numPassesArray.Read(this->curRead, this->curRead+1, &numPasses);
if (numPasses > 0) {
// Read in the ccs bases
if ((retVal = ccsBasReader.GetNext((SMRTSequence&)ccsSequence)) == 0)
return 0;
ccsSequence.numPasses = numPasses;
if (this->includedFields["AdapterHitAfter"]) {
ccsSequence.adapterHitAfter.resize(ccsSequence.numPasses);
adapterHitAfterArray.Read(curPassPos, curPassPos + ccsSequence.numPasses, &ccsSequence.adapterHitAfter[0]);
}
if (this->includedFields["AdapterHitBefore"]) {
ccsSequence.adapterHitBefore.resize(ccsSequence.numPasses);
adapterHitBeforeArray.Read(curPassPos, curPassPos + ccsSequence.numPasses, &ccsSequence.adapterHitBefore[0]);
}
if (this->includedFields["PassDirection"]) {
ccsSequence.passDirection.resize(ccsSequence.numPasses);
passDirectionArray.Read(curPassPos, curPassPos + ccsSequence.numPasses, &ccsSequence.passDirection[0]);
}
if (this->includedFields["PassNumBases"]) {
ccsSequence.passNumBases.resize(ccsSequence.numPasses);
passNumBasesArray.Read(curPassPos, curPassPos + ccsSequence.numPasses, &ccsSequence.passNumBases[0]);
}
if (this->includedFields["PassStartBase"]) {
ccsSequence.passStartBase.resize(ccsSequence.numPasses);
passStartBaseArray.Read(curPassPos, curPassPos + ccsSequence.numPasses, &ccsSequence.passStartBase[0]);
}
if (this->includedFields["PassStartPulse"]) {
ccsSequence.passStartPulse.resize(ccsSequence.numPasses);
passStartPulseArray.Read(curPassPos, curPassPos + ccsSequence.numPasses, &ccsSequence.passStartPulse[0]);
}
if (this->includedFields["PassNumPulses"]) {
ccsSequence.passNumPulses.resize(ccsSequence.numPasses);
passNumPulsesArray.Read(curPassPos, curPassPos + ccsSequence.numPasses, &ccsSequence.passNumPulses[0]);
}
curPassPos += ccsSequence.numPasses;
}
else {
// advance a read in the ccs sequence without advancing positions.
ccsBasReader.curRead++;
}
//
// Regardless whether or not a ccs read was called, read the next
// unrolled read, since an unrolled read is called for each zmw.
//
retVal = ((T_HDFBasReader<SMRTSequence>*)this)->GetNext(ccsSequence.unrolledRead);
ccsSequence.zmwData = ccsSequence.unrolledRead.zmwData;
ccsSequence.CopyTitle(ccsSequence.unrolledRead.title);
string newTitle = string(ccsSequence.title) + string("/ccs");
ccsSequence.CopyTitle(newTitle.c_str());
} catch (H5::DataSetIException e) {
cout << "ERROR, could not read ccs data for CCS Sequence "
<< ccsSequence.unrolledRead.title << endl;
exit(1);
}
// cout << "title: " << ccsSequence.title << endl;
if (retVal == 0) {
return 0;
}
else {
return 1;
}
}