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#include <vector>
#include <string>
#include "NucConversion.hpp"
#include "FASTASequence.hpp"
#include "FASTAReader.hpp"
#include "suffixarray/SuffixArray.hpp"
#include "suffixarray/SuffixArrayTypes.hpp"
#include "suffixarray/ssort.hpp"
#include "algorithms/sorting/qsufsort.hpp"
void PrintUsage() {
cout << "samodify changes word size of input suffix array." << endl;
cout << "Usage: samodify in.sa genome.fasta out.sa [-blt p]" << endl;
cout << " -blt p Build a lookup table on prefixes of length 'p' " << endl;
}
int main(int argc, char* argv[]) {
if (argc < 4) {
PrintUsage();
exit(1);
}
int argi = 1;
string saInFile = argv[argi++];
string genomeFileName = argv[argi++];
string saOutFile = argv[argi++];
vector<string> inFiles;
int doBLT = 0;
int doBLCP = 0;
int bltPrefixLength = 0;
int lcpLength = 0;
int parsingOptions = 0;
while (argi < argc) {
if (strcmp(argv[argi], "-blt") == 0) {
doBLT = 1;
bltPrefixLength = atoi(argv[++argi]);
}
else if (strcmp(argv[argi], "-blcp") == 0) {
doBLCP = 1;
lcpLength = atoi(argv[++argi]);
}
else {
PrintUsage();
cout << "Bad option: " << argv[argi] << endl;
exit(1);
}
++argi;
}
//
// Read the suffix array to modify.
//
DNASuffixArray sa;
sa.Read(saInFile);
FASTAReader reader;
reader.Initialize(genomeFileName);
FASTASequence seq;
reader.ReadAllSequencesIntoOne(seq);
if (doBLT) {
sa.BuildLookupTable(seq.seq, seq.length, bltPrefixLength);
}
if (doBLCP) {
cout << "LCP Table not yet implemented." << endl;
}
sa.Write(saOutFile);
}
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