The run-length matrix using runLengthMatrix executable is available with Margin.
./runLengthMatrix \
<BAM> \
<REF> \
base_params.json \
-t <THREADS> \
-l <highest_runlength_allowed> \
-o OUTPUT_DIR/OUTPUT_PREFIX
base_params.json = https://github.com/UCSC-nanopore-cgl/margin/blob/master/params/base_params.json