16 namespace PacBio {  namespace
92     parser.version(PacBio::BAM::pbbamify::Version);  in main()
124     const PacBio::BAM::pbbamify::Settings settings =  in main()
125         PacBio::BAM::pbbamify::Settings::FromCommandLine(parser, argc, argv);  in main()
139         PacBio::BAM::ProgramInfo pbbamifyProgram;  in main()
140         pbbamifyProgram.Id(std::string("pbbamify-") + PacBio::BAM::pbbamify::Version)  in main()
142             .Version(PacBio::BAM::pbbamify::Version);  in main()
144         PacBio::BAM::DataSet dataset = PacBio::BAM::DataSet(settings.pbbamFilename_);  in main()
145         PacBio::BAM::BamReader inputBamReader(settings.inputFilename_);  in main()
146         PacBio::BAM::BamHeader newHeader;  in main()
150             PacBio::BAM::FastaReader ref_reader(settings.referenceFilename_);  in main()
152                 PacBio::BAM::pbbamify::Pbbamify::ComposeHeader(dataset, ref_reader, inputBamReader);  in main()
155         std::shared_ptr<PacBio::BAM::pbbamify::QueryLookup> queryLookup =  in main()
156             PacBio::BAM::pbbamify::CreateQueryLookup(dataset);  in main()
162             PacBio::BAM::IndexedFastaReader indexedRefReader(settings.referenceFilename_);  in main()
163             PacBio::BAM::BamWriter bamWriter(settings.outputFilename_, newHeader);  in main()
164             bool augment_rv = PacBio::BAM::pbbamify::Pbbamify::AugmentAlignments(  in main()