invalid choice: 'sg-coverage'

[Chris S]

Hello - thank you for this tool. I am in the process of trying to apply Majiq-v3 to some cancer RNAseq data but I am running into issues with the specific commands provided in the documentation. 

In particular, I am unable to run majiq-v3 sg-coverage. I get

```

majiq: error: argument {build,psi-coverage,moccasin,psi,deltapsi,heterogen,cite}: invalid choice: 'sg-coverage' (choose from build, psi-coverage, moccasin, psi, deltapsi, heterogen, cite)

```

My setup is majiq 3.0.10, Python 3.12.11, gcc 15.1.0, htslib 1.22.1. 

Apologies for the very elementary question. 

Thanks

Chris

[Chris S]

For reference, my commands are: 

majiq-build gff3 $gff3 ${output_dir}/annotations/sg.zarr --license $MAJIQ_LICENSE

majiq-build sj a.bam ${output_dir}/annotations/sg.zarr ${output_dir}/sj/.sj --license $MAJIQ_LICENSE

majiq-build update -j 1 --min-experiments 1 ${output_dir}/annotations/sg.zarr ${output_dir}/annotations/updated_sg.zarr --sjs ${output_dir}/sj/.sj --license $MAJIQ_LICENSE

majiq-v3 psi-coverage ${output_dir}/annotations/updated_sg.zarr ${output_dir}/psi/.psicov ${output_dir}/sj/.sj --license $MAJIQ_LICENSE

majiq-v3 quantify ${output_dir}/psi/.psicov --min-experiments 0.01 ${output_dir}/build/sg.zarr --output-tsv ${output_dir}/psi/.tsv --license $MAJIQ_LICENSE

majiq-v3 sg-coverage ${output_dir}/annotations/updated_sg.zarr ${output_dir}/build/.sgc ${output_dir}/sj/.sj --license $MAJIQ_LICENSE

These commands were built using the interactive command builder on your documentation site with some modification in order to work. Unfortunately, the last two commands result in "Invalid choice" and therefore I cannot proceed further. 

Many thanks

Chris

[Chris S]

Dear biociphers team 

Please ignore the above for now - I have been unable to reproduce this bug and have manage to run the steps. 

Kind regards

Chris