4cb89356f40786422b00588a01f29e3425d7d2bf,mro/stages/aggregator/check_molecule_info_version/__init__.py,,split,#Any#,29

Before Change

        else:
            files_seen.add(mol_h5)

        mc_h5 = h5py.File(sample_def[cr_constants.AGG_H5_FIELD], "r")
        try:
            mol_h5_version = mc_h5.attrs[cr_mol_counter.FILE_VERSION_KEY]
        except AttributeError:
            martian.exit("The molecule info HDF5 file (version %d) was produced by an older version of Cell Ranger. Reading these files is unsupported." % mol_h5_version)

After Change

            mc_table = tables.open_file(mc_fn, "r")
            cr_major_version = int(mc_table.get_node("/metrics")._v_attrs["cellranger_version"].split(".", 1)[0])
            mc_table.close()
            if cr_major_version < 2:
                martian.exit("The molecule info HDF5 file (%s) was produced by an older version of Cell Ranger. Reading these files is unsupported." % mc_fn)

            nrows = mc_h5["barcode"].shape[0]
            mem_gb = cr_mol_counter.MoleculeCounter.estimate_mem_gb(nrows, scale=4)
        else: 
            mem_gb = 1

Instances