usage: bigwig_hmm.py [-h] [-i INPUTFILE] [-g GENOME] [-n NUM_STATES] [-o OUTPUTFILE]

Create bedfile of HMM states from bigwig

optional arguments: -h, --help show this help message and exit

-i INPUTFILE, --inputfile INPUTFILE path to the bigwig file(s)

-g GENOME, --genome GENOME genome (i.e. hg38)

-n NUM_STATES, --num_states NUM_STATES number of hidden states

-o OUTPUTFILE, --outputfile OUTPUTFILE output filename (endswith:#_state_HMM.bed)

Wrapper based on https://github.com/jmschrei/pomegranate