count.py 文件源码

def get_loc_reads(bp,bamf,max_dp):
    loc = '%s:%d:%d' % (bp['chrom'], max(0,bp['start']), bp['end'])
    loc_reads = np.empty([0,len(dtypes.read_dtype)],dtype=dtypes.read_dtype)
    err_code = 0
    try:
        iter_loc = bamf.fetch(region=loc,until_eof=True)
        for x in iter_loc:
            read = read_to_array(x,bamf)
            if len(np.atleast_1d(read))>0:
                loc_reads = np.append(loc_reads,read)
            if len(loc_reads) > max_dp:
                print('Read depth too high at %s' % loc)
                err_code = 1
                return np.empty(0), err_code
        loc_reads = np.sort(loc_reads,axis=0,order=['query_name','ref_start'])
        loc_reads = np.unique(loc_reads) #remove duplicates
        return loc_reads, err_code
    except ValueError:
        print('Fetching reads failed for loc: %s' % loc)
        err_code = 2
        return np.empty(0), err_code