def calc_paired_insert_stats(in_bam, nsample=1000000):
    """Retrieve statistics for paired end read insert distances.
    """
    dists = []
    n = 0
    with pysam.Samfile(in_bam, "rb") as in_pysam:
        for read in in_pysam:
            if read.is_proper_pair and read.is_read1:
                n += 1
                dists.append(abs(read.isize))
                if n >= nsample:
                    break
    return insert_size_stats(dists)
def calc_paired_insert_stats ( in_bam , nsample = 1000000 ) : dists = [ ] n = 0 with pysam . Samfile ( in_bam , "rb" ) as in_pysam : for read in in_pysam : if read . is_proper_pair and read . is_read1 : n += 1 dists . append ( abs ( read . isize ) ) if n >= nsample : break return insert_size_stats ( dists )
Retrieve statistics for paired end read insert distances.