fibertools-rs a CLI tool for interacting with fiberseq bam files. The main utility is ft extract which extracts fiberseq data from a bam file into plain text.
$ ft extract --help
ft-extract 0.0.2
Extract fiberseq data into plain text files
USAGE:
ft extract [OPTIONS] [BAM]
ARGS:
<BAM> fiberseq bam file [default: -]
OPTIONS:
-r, --reference report in reference sequence coordinates
-m, --m6a <M6A> Output path for m6a bed12
-c, --cpg <CPG> Output path for CpG (primrose) bed12
-m, --msp <MSP> Output path for methylation sensitive patch (msp) bed12
-n, --nuc <NUC> Output path for nucleosome bed12
-h, --help Print help information
-V, --version Print version information