pysam筛选reads写bam

使用pysam从bam中筛选reads

bamfile = 'Final.bam'
bam = pysam.AlignmentFile(bamfile, "r")
outfile = pysam.AlignmentFile('out.bam', "wb", template=bam)
ALL = set()
for reads in bam:
	status = '''some filters'''
	if status:
        outfile.write(reads)
        print(reads.qname)
        ALL.add(reads.qname)
    else:
    	continue
bam.close()
outfile.close()