opts

Options recognized by all commands

Input options:
    --fmt <format>      Input format: fasta(default), fastq (fastq-illumina,
                        fastq-solexa), or csv / tsv (=txt).
                        Compression: <format>.<compression> (.gz, .bz2 or .lz4).
                        Only needed if format cannot be guessed from extension.
    --fields <fields>   CSV fields: 'id,seq,desc' (in order) or 'id:2,desc:6,seq:9'
                        (col. num.) or headers: 'id:id,seq:sequence,desc:desc'
                        [default: id,seq,desc]
    --delim <delim>     TSV/CSV delimiter. Defaults: '\t' for tsv/txt; ',' for csv
    --header            Specify if CSV file has a header. Auto-enabled with headers.
    --fa                FASTA input. Short for '--fmt fasta'.
    --fq                FASTQ input. Short for '--fmt fastq'.
    --fq-illumina       FASTQ input in Illumina 1.3+ format (--fmt fastq-illumina)
    --csv <fields>      CSV input. Short for '--fmt csv --fields <fields>'
    --tsv <fields>      TSV input. Short for '--fmt tsv --fields <fields>'
    --qual <file>       Path to QUAL file with quality scores (Roche 454 style)

Output options:
    -o, --output <f>    Write output to <file> instead of STDOUT [default: -].
    --to <outformat>    Output format and compression. See --fmt. Only needed
                        if not guessed from the extension (default: input format).
    --wrap <width>      Wrap FASTA sequences to maximum <width> characters
    --out-delim <d>     TSV/CSV delimiter. Defaults: '\t' for tsv/txt; ',' for csv
    --outfields <f>     TSV/CSV fields (variables allowed). [default: id,seq,desc]
    --to-fa             FASTA output. Short for: '--to fasta'
    --to-fq             FASTQ output. Short for: '--to fastq'
    --to-csv <fields>   CSV output. Short for '--to csv --outfields <f>'
    --to-tsv <fields>   TSV output. Short for '--to tsv --outfields <f>'
    --compr-level <l>   Level for compressed output. 1-9 for GZIP/BZIP2 and
                        1-21 for ZSTANDARD
    --qual-out <file>   Path to QUAL output file with quality scores

Attribute options:
    -a, --attr <a>      Add an attribute in the form name=value to FASTA/FASTQ
                        headers (multiple '-a key=value' args possible)
    --adelim <delim>    Attribute delimiter inserted before. If not a space,
                        attributes are appended to the ID (default: ' ')
    --aval-delim <d>    Delimiter between attribute names and values [default: =]

Associated lists:
    -l, --list <path>   Path to list with metadata (multiple -l args possible)
    --ldelim <delim>    Delimiter for list [default: \t]
    --lheader           List contains a header row. Automatically enabled if
                        variables in the form {l:<name>} are found.
    --id-col <no>       ID column number [default: 1]
    -u, --unordered     Allow lists to in different order than sequences.
    -m, --missing       Allow missing rows with '-u'. Variable output is empty.

General Information:
    -v, --verbose       Print more detailed information.
    -h, --help          Display this message
    --help-vars         List and explain all available variables

Advanced Options:
    --buf-cap <size>    Initial capacity of internal reader buffer [default: 68K]
    --max-mem <size>    Buffer size limit. Larger sequences will cause an error.
                        [default: 1G]
    -T, --read-thread   Read from a different thread. Enabled with compressed input.
    --write-thread      Write in a different thread. Enabled with compressed output.
    --read-tbufsize S   Buffer size of threaded reader (default: auto)
    --write-tbufsize S  Buffer size of threaded reader (default: auto)