INNER CODE UNIT · Python

is_pair_end

nloyfer/wgbs_tools · src/python/bam2pat.py:262

def is_pair_end(bam, genome):
    first_line = subprocess.check_output(f'samtools view {bam} -T {genome.genome_path} | head -1', shell=True)
    first_line = first_line.decode()
    if len(first_line) == 0:
        raise EmptyBamError('Empty bam file')
    return int(first_line.split('\t')[1]) & 1


class Bam2Pat:
    def __init__(self, args, bam):
        self.args = args
        self.tmp_dir = None
        self.verbose = args.verbose
        self.out_dir = args.out_dir
        self.bam_path = bam
        self.gr = GenomicRegion(args)
        self.PE = None
        if not self.args.nanopore:

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