int main(int argc, char* argv[]) {
if (argc < 2) {
PrintUsage();
exit(1);
}
int argi = 1;
string saFile = argv[argi++];
vector<string> inFiles;
int doBLT = 1;
int bltPrefixLength = 8;
int parsingOptions = 0;
SAType saBuildType = larsson;
int read4BitCompressed = 0;
int diffCoverSize = 0;
while (argi < argc) {
if (strlen(argv[argi]) > 0 and
argv[argi][0] == '-'){
parsingOptions = 1;
}
if (!parsingOptions) {
inFiles.push_back(argv[argi]);
}
else {
if (strcmp(argv[argi], "-blt") == 0) {
doBLT = 1;
if (argi < argc - 1) {
bltPrefixLength = atoi(argv[++argi]);
if (bltPrefixLength == 0) {
cout << argv[argi] << " is not a valid lookup table length." << endl;
exit(1);
}
}
else {
cout << "Please specify a lookup table length." << endl;
exit(1);
}
}
else if (strcmp(argv[argi], "-mamy") == 0) {
saBuildType = manmy;
}
else if (strcmp(argv[argi], "-larsson") == 0) {
saBuildType = larsson;
}
else if (strcmp(argv[argi], "-mcilroy") == 0) {
saBuildType = mcilroy;
}
else if (strcmp(argv[argi], "-slow") == 0) {
saBuildType = slow;
}
else if (strcmp(argv[argi], "-kark") == 0) {
saBuildType = kark;
}
else if (strcmp(argv[argi], "-mafe") == 0) {
saBuildType = mafe;
}
else if (strcmp(argv[argi], "-welter") == 0) {
saBuildType = welter;
}
else if (strcmp(argv[argi], "-welterweight") == 0) {
if (argi < argc-1) {
diffCoverSize = atoi(argv[++argi]);
}
else {
cout << "Please specify a difference cover size. Valid values are 7,32,64,111, and 2281. Larger values use less memory but may be slower." << endl;
exit(1);
}
if ( ! (diffCoverSize == 7 or
diffCoverSize == 32 or
diffCoverSize == 64 or
diffCoverSize == 111 or
diffCoverSize == 2281) ) {
cout << "The difference cover size must be one of 7,32,64,111, or 2281." << endl;
cout << "Larger numbers use less space but are more slow." << endl;
exit(1);
}
}
else if (strcmp(argv[argi], "-4bit") == 0) {
read4BitCompressed = 1;
}
else {
PrintUsage();
cout << "ERROR, bad option: " << argv[argi] << endl;
exit(1);
}
}
++argi;
}
if (inFiles.size() == 0) {
//
// Special use case: the input file is a fasta file. Write to that file + .sa
//
inFiles.push_back(saFile);
saFile = saFile + ".sa";
}
VectorIndex inFileIndex;
FASTASequence seq;
CompressedSequence<FASTASequence> compSeq;
if (read4BitCompressed == 0) {
for (inFileIndex = 0; inFileIndex < inFiles.size(); ++inFileIndex) {
FASTAReader reader;
reader.Init(inFiles[inFileIndex]);
reader.SetSpacePadding(111);
if (saBuildType == kark) {
//
// The Karkkainen sa building method requires a little extra
// space at the end of the dna sequence so that counting may
// be done mod 3 without adding extra logic for boundaries.
//
}
if (inFileIndex == 0) {
reader.ReadAllSequencesIntoOne(seq);
reader.Close();
}
else {
while(reader.ConcatenateNext(seq)) {
cout << "added " << seq.title << endl;
}
}
}
seq.ToThreeBit();
//seq.ToUpper();
}
else {
assert(inFiles.size() == 1);
cout << "reading compressed sequence." << endl;
compSeq.Read(inFiles[0]);
seq.seq = compSeq.seq;
seq.length = compSeq.length;
compSeq.RemoveCompressionCounts();
cout << "done." << endl;
}
//
// For now, do not allow creation of suffix arrays on sequences > 4G.
//
if (seq.length >= UINT_MAX) {
cout << "ERROR, references greater than " << UINT_MAX << " bases are not supported." << endl;
cout << "Consider breaking the reference into multiple files, running alignment. " << endl;
cout << "against each file, and merging the result." << endl;
exit(1);
}
vector<int> alphabet;
SuffixArray<Nucleotide, vector<int> > sa;
// sa.InitTwoBitDNAAlphabet(alphabet);
// sa.InitAsciiCharDNAAlphabet(alphabet);
sa.InitThreeBitDNAAlphabet(alphabet);
if (saBuildType == manmy) {
sa.MMBuildSuffixArray(seq.seq, seq.length, alphabet);
}
else if (saBuildType == mcilroy) {
sa.index = new SAIndex[seq.length+1];
DNALength i;
for (i = 0; i < seq.length; i++) { sa.index[i] = seq.seq[i] + 1;}
sa.index[seq.length] = 0;
ssort(sa.index, NULL);
for (i = 1; i < seq.length+1; i++ ){ sa.index[i-1] = sa.index[i];};
sa.length = seq.length;
}
else if (saBuildType == larsson) {
sa.LarssonBuildSuffixArray(seq.seq, seq.length, alphabet);
}
else if (saBuildType == kark) {
sa.index = new SAIndex[seq.length];
seq.ToThreeBit();
DNALength p;
for (p = 0; p < seq.length; p++ ){ seq.seq[p]++; }
KarkkainenBuildSuffixArray<Nucleotide>(seq.seq, sa.index, seq.length, 5);
sa.length = seq.length;
}
else if (saBuildType == mafe) {
// sa.MaFeBuildSuffixArray(seq.seq, seq.length);
}
else if (saBuildType == welter) {
if (diffCoverSize == 0) {
sa.LightweightBuildSuffixArray(seq.seq, seq.length);
}
else {
sa.LightweightBuildSuffixArray(seq.seq, seq.length, diffCoverSize);
}
}
if (doBLT) {
sa.BuildLookupTable(seq.seq, seq.length, bltPrefixLength);
}
sa.Write(saFile);
return 0;
}
