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

Before Change

    dframe = (dframe.groupby(by=["chromosome", "strand", "gene"],
                             as_index=False, group_keys=False, sort=False)
              .apply(_merge_overlapping))
    return dframe.reindex()


def _merge_overlapping(dframe):
    Merge overlapping regions within a group.

After Change

                     "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