Parsing GFF_FEATURE

[jfouret]

Hi,

First, thank you for this tool. I may report a small bug, not really a bug though. The parsing of the "gene" feature seems not to be functional as intended originally.
Anyway if we have an ID field, all is good at the end but see below the code to understand what I mean:

PS: It would be good to precise hos the GFF_FEATURE is parsed from the GFF file in the documentation.

You are using the following code:

  std::vector<gff3_feature>::iterator it;
  char *ref_codon, *alt_codon;
  for (it = features.begin(); it != features.end(); it++) {
    fout << line_stream.str();
    // add in gene level info, control for case it's not present
    std::string gene = it->get_attribute("gene");
    if (gene.empty()) {
      fout << it->get_attribute("ID") << "\t";
    } else {
      fout << gene + ":" + it->get_attribute("ID") << "\t";
    }

Why is it not:

  std::vector<gff3_feature>::iterator it;
  char *ref_codon, *alt_codon;
  for (it = features.begin(); it != features.end(); it++) {
    fout << line_stream.str();
    // add in gene level info, control for case it's not present
    std::string gene = it->get_attribute("gene");
    if (gene.empty()) {
      fout << it->get_attribute("ID") << "\t";
    } else {
      fout << gene + ":" + gene << "\t";
    }