def stats_missing_rate_from_hdf5_memory(): fpath = join(TEST_DATA_DIR, 'performance', 'inca_torvum_all_snps.h5') var_mat = VariationsH5(fpath, mode='r') array = VariationsArrays() array.put_chunks(var_mat.iterate_chunks(kept_fields=['/calls/GT'])) calc_stat_by_chunk(array, _MissingGTCalculator())
def stats_missing_rate_from_hdf5(): fpath = join(TEST_DATA_DIR, 'performance', 'inca_torvum_all_snps.h5') h5 = VariationsH5(fpath, mode='r') calc_stat_by_chunk(h5, _MissingGTCalculator())