BamHeader PrepareHeader(const OptionParser& parser, int argc, char** argv,
const vector<string>& files)
{
using boost::algorithm::join;
ProgramInfo program(parser.prog() + "-" + CCS_VERSION);
program.Name(parser.prog())
.CommandLine(parser.prog() + " " + join(vector<string>(argv + 1, argv + argc), " "))
.Description(DESCRIPTION)
.Version(CCS_VERSION);
BamHeader header;
header.PacBioBamVersion("3.0.1").SortOrder("unknown").Version("1.5").AddProgram(program);
for (const auto& file : files) {
BamFile bam(file);
for (const auto& rg : bam.Header().ReadGroups()) {
if (rg.ReadType() != "SUBREAD")
parser.error("invalid input file, READTYPE must be SUBREAD");
ReadGroupInfo readGroup(rg.MovieName(), "CCS");
readGroup.BindingKit(rg.BindingKit())
.SequencingKit(rg.SequencingKit())
.BasecallerVersion(rg.BasecallerVersion())
.FrameRateHz(rg.FrameRateHz());
header.AddReadGroup(readGroup);
}
}
return header;
}
