int main(int argc, char const ** argv)
{
//parse our options
ModifyStringOptions options;
seqan::ArgumentParser::ParseResult res = parseCommandLine(options, argc, argv);
// If parsing was not successful then exit with code 1 if there were errors.
// Otherwise, exit with code 0 (e.g. help was printed).
if (res != seqan::ArgumentParser::PARSE_OK)
return res == seqan::ArgumentParser::PARSE_ERROR;
SeqFileIn seqFileIn;
if (!open(seqFileIn, toCString(options.inputFileName)))
{
std::cerr << "ERROR: Could not open the file.\n";
return 1;
}
CharString id;
Dna5String seq;
CharString qual;
SeqFileOut seqFileOut;
if (!open(seqFileOut, toCString(options.outputFileName)))
{
std::cerr << "ERROR: Could not open the file.\n";
return 1;
}
while(!atEnd(seqFileIn))
{
try
{
readRecord(id, seq, qual, seqFileIn);
}
catch (Exception const & e)
{
std::cout << "ERROR: " << e.what() << std::endl;
return 1;
}
if(length(seq) >= options.length)
{
String<Dna> dnaSeq;
resize(dnaSeq, options.length, Exact());
assign(dnaSeq, seq, Limit());
CharString dnaQual;
resize(dnaQual, options.length, Exact());
assign(dnaQual, qual, Limit());
writeRecord(seqFileOut, id, dnaSeq, dnaQual);
}
}
return 0;
}
PetscErrorCode Solution(TS ts,PetscReal t,Vec X,void *ctx)
{
UserParams *user = (UserParams*)ctx;
PetscReal u,v;
PetscScalar *x;
PetscErrorCode ierr;
PetscFunctionBegin;
Exact(t,user->Omega,user->Xi,user->u0,user->v0,&u,&v);
ierr = VecGetArray(X,&x);CHKERRQ(ierr);
x[0] = (PetscScalar)u;
ierr = VecRestoreArray(X,&x);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
