# Online masking uses RepeatMasker as the search engine in the background, 
# so basically all user parameters of RepeatMasker are retained. We have only made some changes to some parameters.
# For example, the optional value of the - lib parameter is changed to dfam / msRepDB, 
# indicating that the user wants to use dfam library or msRepDB library as the default search library.

    -s  Slow search; 0-5% more sensitive, 2-3 times slower than default

    -q  Quick search; 5-10% less sensitive, 2-5 times faster than default

    -qq Rush job; about 10% less sensitive, 4->10 times faster than default
        (quick searches are fine under most circumstances) repeat options

    -nolow
        Does not mask low_complexity DNA or simple repeats

    -noint
        Only masks low complex/simple repeats (no interspersed repeats)

    -norna
        Does not mask small RNA (pseudo) genes

    -alu
        Only masks Alus (and 7SLRNA, SVA and LTR5)(only for primate DNA)

    -div [number]
        Masks only those repeats < x percent diverged from consensus seq

    -cutoff [number]
        Sets cutoff score for masking repeats when using -lib (default 225)

    Contamination options

    -is_only
        Only clips E coli insertion elements out of fasta and .qual files

    -is_clip
        Clips IS elements before analysis (default: IS only reported)

    -no_is
        Skips bacterial insertion element check

    Running options

    -gc [number]
        Use matrices calculated for 'number' percentage background GC level

    -gccalc
        RepeatMasker calculates the GC content even for batch files/small
        seqs

    -frag [number]
        Maximum sequence length masked without fragmenting (default 60000)

    -nocut
        Skips the steps in which repeats are excised

    -noisy
        Prints search engine progress report to screen (defaults to .stderr
        file)

    -nopost
        Do not postprocess the results of the run ( i.e. call ProcessRepeats
        ). NOTE: This options should only be used when ProcessRepeats will
        be run manually on the results.

    output options

    -a(lignments)
        Writes alignments in .align output file

    -inv
        Alignments are presented in the orientation of the repeat (with
        option -a)

    -lcambig
        Outputs ambiguous DNA transposon fragments using a lower case name.
        All other repeats are listed in upper case. Ambiguous fragments
        match multiple repeat elements and can only be called based on
        flanking repeat information.

    -small
        Returns complete .masked sequence in lower case

    -xsmall
        Returns repetitive regions in lowercase (rest capitals) rather than
        masked

    -x  Returns repetitive regions masked with Xs rather than Ns

    -poly
        Reports simple repeats that may be polymorphic (in file.poly)

    -source
        Includes for each annotation the HSP "evidence". Currently this
        option is only available with the "-html" output format listed
        below.

    -html
        Creates an additional output file in xhtml format.

    -ace
        Creates an additional output file in ACeDB format

    -gff
        Creates an additional Gene Feature Finding format output

    -u  Creates an additional annotation file not processed by
        ProcessRepeats

    -xm Creates an additional output file in cross_match format (for
        parsing)

    -no_id
        Leaves out final column with unique ID for each element (was
        default)

    -e(xcln)
        Calculates repeat densities (in .tbl) excluding runs of >=20 N/Xs in
        the query