def process_fastq_single_end_read_file_no_barcode(fastq_read_f, sample_id, store_unassigned=False, max_bad_run_length=0, phred_quality_threshold=2, min_per_read_length_fraction=0.75, rev_comp=False, seq_max_N=0, start_seq_id=0, filter_bad_illumina_qual_digit=False, log_f=None, histogram_f=None, phred_offset=None):
 fake_barcodes = cycle(['@', 'AAAAAAAAAAAA', '+', 'CCCCCCCCCCCC'])
 barcode_to_sample_id = {'AAAAAAAAAAAA': sample_id}
 for e in process_fastq_single_end_read_file(fastq_read_f, fake_barcodes, barcode_to_sample_id, store_unassigned=store_unassigned, max_bad_run_length=max_bad_run_length, phred_quality_threshold=phred_quality_threshold, min_per_read_length_fraction=min_per_read_length_fraction, rev_comp=rev_comp, rev_comp_barcode=False, seq_max_N=seq_max_N, start_seq_id=start_seq_id, filter_bad_illumina_qual_digit=filter_bad_illumina_qual_digit, log_f=log_f, histogram_f=histogram_f, barcode_correction_fn=None, max_barcode_errors=0, strict_header_match=False, phred_offset=phred_offset):
  (yield e)

def process_fastq_single_end_read_file_no_barcode ( fastq_read_f , sample_id , store_unassigned = False , max_bad_run_length = 0 , phred_quality_threshold = 2 , min_per_read_length_fraction = 0.75 , rev_comp = False , seq_max_N = 0 , start_seq_id = 0 , filter_bad_illumina_qual_digit = False , log_f = None , histogram_f = None , phred_offset = None ) : fake_barcodes = cycle ( [ '@' , 'AAAAAAAAAAAA' , '+' , 'CCCCCCCCCCCC' ] ) barcode_to_sample_id = { 'AAAAAAAAAAAA' : sample_id } for e in process_fastq_single_end_read_file ( fastq_read_f , fake_barcodes , barcode_to_sample_id , store_unassigned = store_unassigned , max_bad_run_length = max_bad_run_length , phred_quality_threshold = phred_quality_threshold , min_per_read_length_fraction = min_per_read_length_fraction , rev_comp = rev_comp , rev_comp_barcode = False , seq_max_N = seq_max_N , start_seq_id = start_seq_id , filter_bad_illumina_qual_digit = filter_bad_illumina_qual_digit , log_f = log_f , histogram_f = histogram_f , barcode_correction_fn = None , max_barcode_errors = 0 , strict_header_match = False , phred_offset = phred_offset ) : ( yield e )
quality filtering when a single sample has been run in a lane this code simulates a barcode file to allow us to re-use the quality filtering code when not demultiplexing .