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#ifndef _BLASR_HDF_CMP_DATA_HPP_
#define _BLASR_HDF_CMP_DATA_HPP_
#include <hdf/HDFAtom.hpp>
#include <hdf/HDFCmpRefAlignmentGroup.hpp>
class HDFCmpData
{
public:
HDFAtom<std::string> commandLine;
H5::H5File hdfCmpFile;
HDFArray<int> movieNameIdArray;
HDFStringArray movieNameArray;
HDFStringArray readGroupPathArray;
HDFArray<int> readGroupPathIdArray;
HDFArray<int> refSeqNameIdArray;
HDFStringArray refSeqNameArray;
static const int NCols = 22;
std::vector<HDFAtom<std::string> > colNameAtoms;
std::vector<HDFCmpRefAlignmentGroup *> refAlignGroups;
std::map<std::string, int> nameToAlignmentGroupIndex;
static const char *colNameIds[];
void Close() { hdfCmpFile.close(); }
};
const char *HDFCmpData::colNameIds[] = {"00", "01", "02", "03", "04", "05", "06", "07",
"08", "09", "10", "11", "12", "13", "14", "15",
"16", "17", "18", "19", "20", "21"};
#endif
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