optional arguments:

-h, --help

show this help message and exit

-d MIN_READ_DEPTH, --min_read_depth MIN_READ_DEPTH

minimum coverage of position to determine methylation (default = 15)

-t MOD_THRESHOLD, --mod_threshold MOD_THRESHOLD

minimum fraction of observations with probability of methylation >=50% at a position to include in report (default = 0.5)

-f MCALLER_FILE, --mCaller_file MCALLER_FILE

the output file from mCaller to summarize

-p POSITIONS, --positions POSITIONS

~bed file of positions for which to calculate % of methylated reads (chromosome,start,end,strand); ignores other thresholds

--control

take unmethylated positions as a control for motif detection

--gff

output PacBio-style gff instead of bed ("identificationQv" score will be average probability of methylation)

--ref REF

use reference fasta to output longer contexts surrounding a base, from -20 to +20

--plot

plot currents deviations at the positions included (not recommended for many positions)

--plotsummary

plot currents deviations summarized across the positions included

--plotdir PLOTDIR

output directory for plots, default=mCaller_position_plots

--vo

verbose output including probabilities for each position

-v, --version

print version