$ rnftools mason2rnf -h

usage: rnftools mason2rnf [-h] -s file -o file -i file [-g int] [-u] [-n str]

Convert a Mason SAM file to RNF-FASTQ.

optional arguments:
  -h, --help            show this help message and exit
  -s file, --sam file   Input SAM/BAM with true (expected) alignments of the
                        reads (- for standard input).
  -o file, --rnf-fastq file
                        Output FASTQ file (- for standard output).
  -i file, --fasta-index file
                        FAI index of the reference FASTA file (- for standard
                        input). It can be created using 'samtools faidx'.
  -g int, --genome-id int
                        Genome ID in RNF (default: 1).
  -u, --allow-unmapped  Allow unmapped reads.
  -n str, --simulator-name str
                        Name of the simulator (for RNF).
