assembler.py 文件源码

def _get_read_alignments(f: TextIO, reads: ReadMapping) -> AlignmentsT:
    logger.info("Pass 2 of alignments GFA2 file to import all pairwise local "
                "alignments...")
    read_alignments = defaultdict(dict)

    la_iter = map(gfa.gfa2_line_to_la(reads),
                  (l for l in f if l.startswith('E')))

    for la in la_iter:
        a_read, b_read = la.get_oriented_reads()
        read_alignments[a_read][b_read] = la
        read_alignments[b_read][a_read] = la.switch()

    logger.info("Done.")

    return read_alignments