// 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
mc_table = tables.open_file(mc_fn, "r")
mc_attrs = mc_table.get_node("/metrics")._v_attrs
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]
