prepare-ref only accepts '-o', not '--out' option

[jfass]

using current commit, in a docker / conda environment

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docker run --rm -v pwd:/data -w /data rna-hla-hlapers
/bin/bash -c '/opt/conda run --no-capture-output -n hp-env
hlapers prepare-ref
--transcripts ref/gencode.v21.pc_transcripts.fa
--annotations ref/gencode.v21.annotation.gtf
--imgt ref/IMGTHLA
--out ref/hlapers'
ERROR: unknown parameter --out
Usage: hlapers prepare-ref [options]

-t | --transcripts Fasta with Gencode transcript sequences.
-a | --annotations GTF from Gencode for the same Genome version.
-i | --imgt Path to IMGT directory.
-o | --out Output directory.
ERROR conda.cli.main_run:execute(41): conda run hlapers prepare-ref --transcripts ref/gencode.v21.pc_transcripts.fa --annotations ref/gencode.v21.annotation.gtf -- imgt ref/IMGTHLA --out ref/hlapers failed. (See above for error)
##############

(when modified to '-o ref/hlapers', it works)

[jfass]

... also bam2fq only accepts "-m", not "--mhc-coords"