$ rnftools liftover -h

usage: rnftools liftover [-h] [-c file] -g int [-x file] [--invert]
                         [--input-format str] [--output-format str]
                         input output

Liftover genomic coordinates in RNF names in a SAM/BAM files or in a FASTQ
file.

positional arguments:
  input                 Input file to be transformed (- for standard input).
  output                Output file to be transformed (- for standard output).

optional arguments:
  -h, --help            show this help message and exit
  -c file, --chain file
                        Chain liftover file for coordinates transformation.
                        [no transformation]
  -g int, --genome-id int
                        ID of genome to be transformed.
  -x file, --faidx file
                        Fasta index of the reference sequence. [extract from
                        chain file]
  --invert              Invert chain file (transformation in the other
                        direction).
  --input-format str    Input format (SAM/BAM/FASTQ). [autodetect]
  --output-format str   Output format (SAM/BAM/FASTQ). [autodetect]
