from frst.dependences import pybam

def parse_bam(bam_file):
    cov = {}
    cov_val = 0
    for alignment in pybam.read(bam_file):
        #pos 1 based (see Pybam doc)
        start_pos = alignment.sam_pos1
        end_pos = alignment.sam_pos1 + alignment.sam_block_size
        if start_pos not in cov:
            cov[start_pos] = 0
        if end_pos not in cov:
            cov[end_pos] = 0
        # add a weight on the start and lower on the end
        cov[start_pos] = cov_val +1
        cov[end_pos] = cov_val -1
    return cov