optional arguments:

-h, --help

show this help message and exit

-p POSITIONS, --positions POSITIONS

file with a list of positions at which to classify bases (must be formatted as space- or tab-separated file with chromosome, position, strand, and label if training)

-m MOTIF, --motif MOTIF

classify every base of type --base in the motif specified instead (can be single one-mer)

-r REFERENCE, --reference REFERENCE

fasta file with reference aligned to

-e TSV, --tsv TSV

tsv file with nanopolish event alignment

-f FASTQ, --fastq FASTQ

fastq file with nanopore reads

-t THREADS, --threads THREADS

specify number of processes (default = 1)

-b BASE, --base BASE

bases to classify as methylated or unmethylated (A or C, default A)

-n NUM_VARIABLES, --num_variables NUM_VARIABLES

change the length of the context used to classify (default of 6 variables corresponds to 11-mer context (6*2-1))

--train

train a new model (requires labels in positions file)

--training_tsv TRAINING_TSV

mCaller output file for training

-d MODELFILE, --modelfile MODELFILE

model file name

-s SKIP_THRESH, --skip_thresh SKIP_THRESH

number of skips to allow within an observation (default 0)

-q QUAL_THRESH, --qual_thresh QUAL_THRESH

quality threshold for reads (default none)

-c CLASSIFIER, --classifier CLASSIFIER

use alternative classifier: options = NN (default), RF, LR, or NBC (non-default may significantly increase runtime)

--plot_training

plot probabilities distributions for training positions (requires labels in positions file and --train)

-v, --version

print version