2793951b051283cc051b8ba4afaed511c58b5d5a,anvio/bamops.py,,_get_aligned_sequence_and_reference_positions,#Any#Any#Any#Any#,986

Before Change

    ref_consumed, read_consumed = 0, 0
    num_mapped = 0
    for operation, length, consumes_read, consumes_ref in iterate_cigartuples(cigartuples, cigar_consumption):

        if consumes_read and consumes_ref:
            aligned_sequence[num_mapped:num_mapped+length] = query_sequence[read_consumed:(read_consumed + length)]
            reference_positions[num_mapped:num_mapped+length] = np.arange(ref_consumed + reference_start, ref_consumed + reference_start + length)

            num_mapped += length
            read_consumed += length
            ref_consumed += length

        elif consumes_ref:
            ref_consumed += length

        elif consumes_read:
            read_consumed += length

    return aligned_sequence, reference_positions


@jit(nopython=True)

After Change

    ref_consumed, read_consumed = 0, 0
    num_mapped = 0
    for i in range(cigartuples.shape[0]):
        operation, length = cigartuples[i, :]
        consumes_read, consumes_ref = cigar_consumption[operation, :]

        if consumes_read and consumes_ref:
            aligned_sequence[num_mapped:num_mapped+length] = query_sequence[read_consumed:(read_consumed + length)]
            reference_positions[num_mapped:num_mapped+length] = np.arange(ref_consumed + reference_start, ref_consumed + reference_start + length)

            num_mapped += length
            read_consumed += length
            ref_consumed += length

        elif consumes_ref:
            ref_consumed += length

        elif consumes_read:
            read_consumed += length

    return aligned_sequence, reference_positions


@jit(nopython=True, cache=True)

Instances