int main(int argc, char* argv[]) {
if (argc < 3) {
cout << "usage: testBuildOccBins genomeFileName suffixArray" << endl;
exit(0);
}
string genomeFileName = argv[1];
string suffixArrayFileName = argv[2];
FASTAReader reader;
reader.Init(genomeFileName);
FASTASequence seq;
reader.GetNext(seq);
DNASuffixArray suffixArray;
suffixArray.Read(suffixArrayFileName);
Bwt<PackedDNASequence, FASTASequence> bwt;
//bwt.InitializeFromSuffixArray(seq, suffixArray.index);
bwt.InitializeBWTStringFromSuffixArray(seq, suffixArray.index);
bwt.occ.Initialize(bwt.bwtSequence, 4096, 64);
bwt.occ.PrintBins(cout);
}
int main(int argc, char* argv[]) {
if (argc < 3) {
cout << "usage: bwtLocateList bwtName querySeqFile" << endl;
exit(1);
}
string bwtFileName = argv[1];
string querySeqFileName = argv[2];
bool doPrintResults = false;
int maxCount = 0;
int argi = 3;
bool countOnly = false;
while(argi < argc) {
if (strcmp(argv[argi], "-print") == 0) {
doPrintResults = true;
}
else if (strcmp(argv[argi], "-max") == 0) {
maxCount = atoi(argv[++argi]);
}
else if (strcmp(argv[argi], "-count") == 0) {
countOnly = true;
}
else {
cout << "bad option: " << argv[argi] << endl;
}
++argi;
}
Bwt<PackedDNASequence, FASTASequence> bwt;
bwt.Read(bwtFileName);
FASTAReader queryReader;
queryReader.Init(querySeqFileName);
FASTASequence seq;
int seqIndex = 0;
vector<DNALength> positions;
while(queryReader.GetNext(seq)) {
positions.clear();
if (countOnly == false) {
bwt.Locate(seq, positions, maxCount);
}
else {
DNALength sp,ep;
bwt.Count(seq, sp, ep);
}
// cout << "matched " << positions.size() << " positions." << endl;
if (doPrintResults) {
int i;
for (i = 0; i < positions.size(); i++ ){
cout << positions[i] << " ";
}
cout << endl;
}
++seqIndex;
}
// float wordCountsPerLookup = (bwt.bwtSequence.nCountInWord *1.0) / bwt.bwtSequence.nCountNuc;
// cout << "word counts per lookup: " << wordCountsPerLookup << endl;
return 0;
}
int main(int argc, char* argv[]) {
if (argc < 2) {
cout << "usage: printpbbwt in.bwt" << endl;
exit(0);
}
string bwtFileName = argv[1];
Bwt<PackedDNASequence, FASTASequence> bwt;
bwt.Read(bwtFileName);
bwt.bwtSequence.PrintUnpacked(cout);
return 0;
}
int main(int argc, char* argv[]) {
string bwtFileName, saFileName;
if (argc < 3) {
cout << "usage: bwt2sa bwtfile safile " << endl;
exit(1);
}
bwtFileName = argv[1];
saFileName = argv[2];
Bwt<PackedDNASequence, FASTASequence> bwt;
DNASuffixArray suffixArray;
bwt.Read(bwtFileName);
suffixArray.AllocateSuffixArray(bwt.bwtSequence.length-1);
SAIndex index;
for (index = 1; index < bwt.bwtSequence.length+1; index++) {
suffixArray.index[index-1] = bwt.Locate(index);
}
suffixArray.Write(saFileName);
}
