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#include <string>
#include <alignment/utils/FileOfFileNames.hpp>
#include <pbdata/CommandLineParser.hpp>
#include <pbdata/FASTAReader.hpp>
#include <pbdata/metagenome/SequenceIndexDatabase.hpp>
#include <pbdata/utils.hpp>
int main(int argc, char* argv[])
{
CommandLineParser clp;
std::string fastaFileName, indexFileName;
std::vector<std::string> fastaFileNames;
std::vector<std::string> opts;
clp.SetProgramName("bsdb");
clp.SetProgramSummary(
"Build an index database on a file of sequences.\n"
" The index is used to map to reads given alignment positions.\n");
clp.RegisterStringOption("fasta", &fastaFileName, "A file with sequences to build an index.");
clp.RegisterStringOption("index", &indexFileName, "The index file.");
clp.RegisterPreviousFlagsAsHidden();
clp.ParseCommandLine(argc, argv, opts);
std::ifstream fastaIn;
std::ofstream indexOut;
if (FileOfFileNames::IsFOFN(fastaFileName)) {
FileOfFileNames::FOFNToList(fastaFileName, fastaFileNames);
} else {
fastaFileNames.push_back(fastaFileName);
}
CrucialOpen(indexFileName, indexOut, std::ios::out | std::ios::binary);
SequenceIndexDatabase<FASTASequence> seqDB;
for (size_t fileNameIndex = 0; fileNameIndex < fastaFileNames.size(); fileNameIndex++) {
FASTAReader reader;
FASTASequence seq;
reader.Init(fastaFileNames[fileNameIndex]);
int i = 0;
while (reader.GetNext(seq)) {
seqDB.AddSequence(seq);
i++;
}
}
seqDB.Finalize();
seqDB.WriteDatabase(indexOut);
return 0;
}
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