You must specify an input file of a directory path to a set of input files. clone_filter 1.35 clone_filter [-f in_file | -p in_dir [-P] [-I] | -1 pair_1 -2 pair_2] -o out_dir [-i type] [-y type] [-D] [-h] f: path to the input file if processing single-end sequences. p: path to a directory of files. P: files contained within directory specified by '-p' are paired. 1: first input file in a set of paired-end sequences. 2: second input file in a set of paired-end sequences. i: input file type, either 'bustard' for the Illumina BUSTARD output files, 'fastq', 'fasta', 'gzfasta', or 'gzfastq' (default 'fastq'). o: path to output the processed files. y: output type, either 'fastq' or 'fasta' (default fastq). D: capture discarded reads to a file. h: display this help messsage. --oligo_len_1 len: length of the single-end oligo sequence in data set. --oligo_len_2 len: length of the paired-end oligo sequence in data set. --retain_oligo: do not trim off the random oligo sequence (if oligo is inline). Oligo sequence options: --inline_null: random oligo is inline with sequence, occurs only on single-end read (default). --null_index: random oligo is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided). --index_null: random oligo is provded in FASTQ header (Illumina i5 or i7 read). --inline_inline: random oligo is inline with sequence, occurs on single and paired-end read. --index_index: random oligo is provded in FASTQ header (Illumina i5 and i7 read). --inline_index: random oligo is inline with sequence on single-end read and second oligo occurs in FASTQ header. --index_inline: random oligo occurs in FASTQ header (Illumina i5 or i7 read) and is inline with sequence on single-end read (if single read data) or paired-end read (if paired data).