本文整理汇总了C++中CommandLine::add_valid_parm方法的典型用法代码示例。如果您正苦于以下问题：C++ CommandLine::add_valid_parm方法的具体用法？C++ CommandLine::add_valid_parm怎么用？C++ CommandLine::add_valid_parm使用的例子？那么, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类CommandLine的用法示例。
在下文中一共展示了CommandLine::add_valid_parm方法的1个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的C++代码示例。
示例1: main
int main(int argc,char **argv) {
CommandLine *parms = CommandLine::Instance();
parms->add_valid_parm("ref","Reference sequence for alignment");
parms->add_valid_parm("seq","Sequences to align (fastq)");
cout << "SmallAlign" << endl;
cout << parms->usage() << endl;
parms->process_args (argc, argv);
SmallAlign<> aligner(true);
//Perform alignment, calculate error rate
// Load reference sequence
FastaReader<> reference_fastafile(parms->get_parm("ref"));
bool openok = reference_fastafile.open();
if(openok == false) cerr << "Could not open reference file: " << parms->get_parm("ref") << endl;
else cerr << "Opened reference file: " << parms->get_parm("ref") << endl;
bool fasta_eof=false;
if(openok) {
for(;!fasta_eof;) {
FastaSequence reference = reference_fastafile.next_sequence(fasta_eof);
if(!fasta_eof) {
// Forward and Reverse? (true/false)
aligner.add_reference(reference.sequence,true);
}
}
}
FastPrbReader<BaseProbability<4> > sequences_fastq(parms->get_parm("seq"));
openok=true;
if(openok == false) cerr << "Could not open sequences file: " << parms->get_parm("seq") << endl;
else cerr << "Opened sequences file: " << parms->get_parm("seq") << endl;
fasta_eof=false;
int max_cycles=40;
int max_quality=100;
int printevery=1000;
vector<int> errors_by_cycle(max_cycles,0);
vector<int> errors_by_quality(max_quality,0);
vector<int> quality_count(max_quality,0);
vector<int> total_by_cycle (max_cycles,0);
vector<int> errors_count(max_cycles,0);
if(openok) {
int n=0;
for(;!sequences_fastq.eof();) {
ProbabilitySequence<BaseProbability<4> > seq = sequences_fastq.get_sequence();
SequenceAlignment<> alm;
alm = aligner.align(seq.string_sequence());
if(alm.score > 30)
for(unsigned int m=0;m<alm.matchstring.size();m++) {
if(alm.matchstring[m] == false) {
errors_by_quality[seq.sequence()[m].max_probability()*max_quality]++;
errors_by_cycle[m]++;
}
quality_count[seq.sequence()[m].max_probability()*max_quality]++;
total_by_cycle[m]++;
}
errors_count[alm.score]++;
if((n%printevery == 0) || sequences_fastq.eof()) {
// Errors by cycle
cout << "Error rates" << endl;
for(int cycle=0;(cycle < max_cycles) && (total_by_cycle[cycle] > 0);cycle++) {
cout << setw(5) << cycle << " ";
cout << setw(10) << (static_cast<double>(errors_by_cycle[cycle])/static_cast<double>(total_by_cycle[cycle]))*100 << " ";
cout << setw(10) << errors_by_cycle[cycle] << " ";
cout << setw(10) << total_by_cycle[cycle] << endl;
}
cout << "Score count" << endl;
for(int errs=0;(errs < max_cycles);errs++) {
cout << setw(5) << errs << " ";
cout << setw(10) << errors_count[errs] << endl;
}
// Errors by quality
cout << "Error by quality" << endl;
for(int quality=0;(quality < max_quality);quality++) {
if(quality_count[quality] != 0) {
cout << setw(5) << quality << " ";
cout << setw(5) << errors_by_quality[quality] << " ";
cout << setw(5) << quality_count[quality] << " ";
cout << setw(10) << 1-(static_cast<double>(errors_by_quality[quality])/static_cast<double>(quality_count[quality])) << endl;
}
}
}
n++;
}
} else {
//.........这里部分代码省略.........