8b9ffbfdec1a9b6daf7b47f63fc2656e3e267c25,mro/stages/aggregator/check_molecule_info_version/__init__.py,,split,#Any#,30

Before Change

            // CRv1.3-generated files lack essential metrics introduced in CRv2 (force_cells, conf_mapped_filtered_bc_reads)
            //   hence aggregation with these files is unsupported
            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)

After Change

            cr_major_version = int(mc_attrs["cellranger_version"].split(".", 1)[0])
            gem_metrics = dict(mc_attrs["gem_groups"])
            mc_table.close()
            if cr_major_version < 2 or not all("conf_mapped_filtered_bc_reads" in group for group in gem_metrics.itervalues()):
                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]

Instances