def paired_reader_from_bamfile(args,
                               log,
                               usage_logger,
                               annotated_writer):
    '''Given a BAM file, return a generator that yields filtered, paired reads'''
    total_aligns = pysamwrapper.total_align_count(args.input_bam)
    bamfile_generator  = _bamfile_generator(args.input_bam)
    return _paired_reader(args.umt_length,
                          bamfile_generator,
                          total_aligns,
                          log,
                          usage_logger,
                          annotated_writer)
def paired_reader_from_bamfile ( args , log , usage_logger , annotated_writer ) : total_aligns = pysamwrapper . total_align_count ( args . input_bam ) bamfile_generator = _bamfile_generator ( args . input_bam ) return _paired_reader ( args . umt_length , bamfile_generator , total_aligns , log , usage_logger , annotated_writer )
Given a BAM file, return a generator that yields filtered, paired reads