gfa.py 文件源码

def gfa2_line_to_la(reads: Mapping[str, Read]):
    def mapper(line: str):
        if not line.startswith('E'):
            raise ValueError('Given GFA2 line is not an edge.')

        sid1, sid2, arange, brange, alignment, tags = gfa2_parse_edge(line)

        a_read = reads[sid1[:-1]]
        b_read = reads[sid2[:-1]]

        return LocalAlignment(
            a_read.with_orientation(sid1[-1]),
            b_read.with_orientation(sid2[-1]),
            arange, brange, alignment)

    return mapper