07d2442c2bfe4521b6e88bb63dc484efac9a53e4,cnvlib/tabio/genepred.py,,read_refflat,#Any#Any#Any#,80

Before Change

            dframe["end"] = dframe["end_cds"].astype("int")
        else:
            dframe["start"] = dframe["start"].astype("int") - 1
            dframe["end"] = dframe["end"].astype("int")

    for key in ("start_cds", "end_cds", "exon_starts", "exon_ends"):
        del dframe[key]
    // NB: same gene name can appear on alt. contigs
    dframe = (dframe.groupby(by=["chromosome", "strand", "gene"],
                             as_index=False, group_keys=False, sort=False)
              .apply(_merge_overlapping))

After Change

    cols_shared = ["gene", "accession", "chromosome", "strand"]
    if exons:
        cols_rest = ["_start_tx", "_end_tx",  // Transcription
                     "_start_cds", "_end_cds",  // Coding region
                     "exon_count", "exon_starts", "exon_ends"]
    elif cds:
        // Use CDS instead of transcription region
        cols_rest = ["_start_tx", "_end_tx",
                     "start", "end",
                     "_exon_count", "_exon_starts", "_exon_ends"]
    else:
        cols_rest = ["start", "end",
                     "_start_cds", "_end_cds",
                     "_exon_count", "_exon_starts", "_exon_ends"]
    colnames = cols_shared + cols_rest
    usecols = [c for c in colnames if not c.startswith("_")]
    // Parse the file contents
    try:
        dframe = pd.read_table(infile,  header=None,

Instances