Fiber-seq toolkit in rust

Usage: ft [OPTIONS] <COMMAND>

Commands:
  predict-m6a       Predict m6A positions using HiFi kinetics data and encode the results in the MM and ML bam tags. Also adds nucleosome (nl, ns) and MTase sensitive patches (al, as) [aliases: m6A, m6a]
  add-nucleosomes   Add nucleosomes to a bam file with m6a predictions
  fire              Add FIREs (Fiber-seq Inferred Regulatory Elements) to a bam file with m6a predictions
  extract           Extract fiberseq data into plain text files [aliases: ex, e]
  center            This command centers fiberseq data around given reference positions. This is useful for making aggregate m6A and CpG observations, as well as visualization of SVs [aliases: c, ct]
  footprint         Infer footprints from fiberseq data
  track-decorators  Make decorated bed files for fiberseq data
  clear-kinetics    Remove HiFi kinetics tags from the input bam file
  strip-basemods    Strip out select base modifications
  help              Print this message or the help of the given subcommand(s)

Options:
  -h, --help     Print help
  -V, --version  Print version

Global-Options:
  -t, --threads <THREADS>  Threads [default: 8]

Debug-Options:
  -v, --verbose...  Logging level [-v: Info, -vv: Debug, -vvv: Trace]
      --quiet       Turn off all logging