01de423a0847bb27ba136764aace9323cd7886a4,hicexplorer/hicCompartmentalization.py,,main,#Any#,170

Before Change

    args = parse_arguments().parse_args(args)

    pc1_bedgraph = pd.read_table(args.pca, header=None, sep="\t")
    pc1 = pd.DataFrame(pc1_bedgraph.values, columns=["chr", "start", "end",
                                                     "pc1"])
    if args.outliers != 0:
        quantile = [args.outliers / 100, (100 - args.outliers) / 100]
        boundaries = np.nanquantile(pc1["pc1"].values.astype(float), quantile)
        quantiled_bins = np.linspace(boundaries[0], boundaries[1],

After Change

    pc1 = pd.read_table(args.pca, header=None, sep="\t",
                        dtype={0: "object", 1: "Int64", 2: "Int64", 3: "float32"})

    pc1 = pc1.rename(columns={0: "chr", 1: "start", 2: "end", 3: "pc1"})

    if args.outliers != 0:
        quantile = [args.outliers / 100, (100 - args.outliers) / 100]
        boundaries = np.nanquantile(pc1["pc1"].values.astype(float), quantile)

Instances