int main(int argc, char* argv[]) {
string barcodeFileName, insertFileName, outputFileName;
if (argc != 4) {
cout << "usage: makeBarcodeDatabase insert.fasta barcodes.fasta output.fasta" << endl;
exit(1);
}
insertFileName = argv[1];
barcodeFileName = argv[2];
outputFileName = argv[3];
FASTAReader barcodeReader, insertReader;
barcodeReader.Initialize(barcodeFileName);
insertReader.Initialize(insertFileName);
ofstream barcodedOut;
CrucialOpen(outputFileName, barcodedOut, std::ios::out);
vector<FASTASequence> forwardBarcodes, reverseBarcodes;
FASTASequence barcodeSequence, reverseBarcodeSequence;
while(barcodeReader.GetNext(barcodeSequence)) {
forwardBarcodes.push_back(barcodeSequence);
barcodeSequence.MakeRC(reverseBarcodeSequence);
reverseBarcodes.push_back(reverseBarcodeSequence);
}
FASTASequence insert;
insertReader.GetNext(insert);
int i;
for (i = 0; i < forwardBarcodes.size(); i++) {
FASTASequence barcodedInsert;
barcodedInsert.Resize(forwardBarcodes[i].length * 2 + insert.length);
stringstream titleStrm;
titleStrm << insert.title << "|ff|" << forwardBarcodes[i].title;
barcodedInsert.CopyTitle(titleStrm.str());
memcpy(&barcodedInsert.seq[0], &forwardBarcodes[i].seq[0], forwardBarcodes[i].length);
memcpy(&barcodedInsert.seq[forwardBarcodes[i].length], insert.seq, insert.length);
memcpy(&barcodedInsert.seq[forwardBarcodes[i].length + insert.length], forwardBarcodes[i].seq, forwardBarcodes[i].length);
barcodedInsert.PrintSeq(barcodedOut);
titleStrm.str("");
titleStrm << insert.title << "|fr|" << forwardBarcodes[i].title;
barcodedInsert.CopyTitle(titleStrm.str());
memcpy(&barcodedInsert.seq[0], &forwardBarcodes[i].seq[0], forwardBarcodes[i].length);
memcpy(&barcodedInsert.seq[forwardBarcodes[i].length], insert.seq, insert.length);
memcpy(&barcodedInsert.seq[forwardBarcodes[i].length + insert.length], reverseBarcodes[i].seq, reverseBarcodes[i].length);
barcodedInsert.PrintSeq(barcodedOut);
titleStrm.str("");
titleStrm << insert.title << "|rf|" << forwardBarcodes[i].title;
barcodedInsert.CopyTitle(titleStrm.str());
memcpy(&barcodedInsert.seq[0], &reverseBarcodes[i].seq[0], reverseBarcodes[i].length);
memcpy(&barcodedInsert.seq[reverseBarcodes[i].length], insert.seq, insert.length);
memcpy(&barcodedInsert.seq[reverseBarcodes[i].length + insert.length], forwardBarcodes[i].seq, forwardBarcodes[i].length);
barcodedInsert.PrintSeq(barcodedOut);
titleStrm.str("");
titleStrm << insert.title << "|rr|" << forwardBarcodes[i].title;
barcodedInsert.CopyTitle(titleStrm.str());
memcpy(&barcodedInsert.seq[0], &reverseBarcodes[i].seq[0], reverseBarcodes[i].length);
memcpy(&barcodedInsert.seq[reverseBarcodes[i].length], insert.seq, insert.length);
memcpy(&barcodedInsert.seq[reverseBarcodes[i].length + insert.length], reverseBarcodes[i].seq, reverseBarcodes[i].length);
barcodedInsert.PrintSeq(barcodedOut);
}
}
GenomeLength FASTAReader::ReadAllSequencesIntoOne(FASTASequence &seq, SequenceIndexDatabase<FASTASequence> *seqDBPtr) {
seq.Free();
GenomeLength p = curPos;
AdvanceToTitleStart(p);
CheckValidTitleStart(p);
ReadTitle(p, seq);
if (seq.title == NULL) {
cout << "ERROR, sequence must have a nonempty title." << endl;
exit(1);
}
if (seqDBPtr != NULL) {
seqDBPtr->growableName.push_back(seq.title);
}
GenomeLength seqLength;
seqLength = fileSize - p;
GenomeLength memorySize = seqLength+padding+1;
if (memorySize > UINT_MAX) {
cout << "ERROR! Reading fasta files greater than 4Gbytes is not supported." << endl;
exit(1);
}
seq.Resize(memorySize);
GenomeLength i;
i = 0L;
for (; p < fileSize; p++, i++ ) {
seq.seq[i] = filePtr[p];
}
i = p = 0;
while (p < seqLength) {
//
// If this is the beginning of another read, add an 'N'
// to delineate spaces between reads.
//
while (p < seqLength and
(seq.seq[p] == ' ' or
seq.seq[p] == '\n' or
seq.seq[p] == '\t' or
seq.seq[p] == '\r')) {
p++;
}
if (p < seqLength and seq.seq[p] == '>') {
seq.seq[i] = 'N';
GenomeLength titleStartPos = p+1;
i++;
while (p < seqLength and seq.seq[p] != '\n') p++;
if (seqDBPtr != NULL and p < seqLength) {
string title;
GenomeLength tp;
for (tp = titleStartPos; tp < p; tp++) {
title.push_back(seq.seq[tp]);
}
seqDBPtr->growableName.push_back(title);
seqDBPtr->growableSeqStartPos.push_back(i);
int nSeq = seqDBPtr->growableSeqStartPos.size();
if (nSeq > 1 and computeMD5) {
string md5Str;
MakeMD5((const char*) &seq.seq[seqDBPtr->growableSeqStartPos[nSeq-2]],
seqDBPtr->growableSeqStartPos[nSeq-1] - seqDBPtr->growableSeqStartPos[nSeq-2] - 1,
md5Str);
seqDBPtr->md5.push_back(md5Str);
}
}
}
else if (p < seqLength) {
// Otherwise, p may be at whitespace
// advance past that as well.
seq.seq[i] = convMat[seq.seq[p]];
i++;
p++;
}
}
if (i > UINT_MAX) {
cout << "ERROR! Sequences greater than 4Gbase are not supported." << endl;
exit(1);
}
//
// Append an 'N' at the end of the last sequence for consistency
// between different orderings of reference input.
//
seq.seq[i] = 'N';
i++;
seq.length = i;
// fill padding.
for (; i < memorySize; i++ ){
seq.seq[i] = 0;
}
seq.deleteOnExit = true;
if (seqDBPtr != NULL) {
seqDBPtr->growableSeqStartPos.push_back(seq.length);
int nSeq = seqDBPtr->growableSeqStartPos.size();
if (nSeq > 1 and computeMD5) {
string md5Str;
MakeMD5((const char*) &seq.seq[seqDBPtr->growableSeqStartPos[nSeq-2]],
seqDBPtr->growableSeqStartPos[nSeq-1] - seqDBPtr->growableSeqStartPos[nSeq-2] - 1,
md5Str);
seqDBPtr->md5.push_back(md5Str);
}
seqDBPtr->Finalize();
}
return seq.length;
}