coverage.py 文件源码

def get_depth_info(read_iter, chrom, cstart, cend):

    depths = np.zeros(cend-cstart, np.int32)

    for read in read_iter:
        pos = read.pos
        rstart = max(pos, cstart)

        # Increment to the end of the window or the end of the
        # alignment, whichever comes first
        rend = min(read.aend, cend)
        depths[(rstart-cstart):(rend-cstart)] += 1

    positions = np.arange(cstart, cend, dtype=np.int32)

    depth_df = pd.DataFrame({"chrom": chrom, "pos": positions, "coverage": depths})
    return depth_df