tview is not included in the docker

[gudedsh]

Subject of the issue

I want to use the tview package under Jvarkit, but after downloading it I realized that this package is not included in the docker (https://hub.docker.com/r/lindenb/jvarkit/tags), how should I get this package? Thank you very much.

[lindenb]

@gudedsh Hi, sorry about this, I don't plan to update docker (I haven't updated it for years) and I'm afraid I forgot to include it in "big" java archive. I've just updated the code, it will be included in the next release.

you can always use the good old "samtools tview" or a tool like "wally".

[gudedsh]

@lindenb Thank you for your reply. I am trying to output the alignment view with the read IDs and output in text format, so I can check which reads specifically contributed to the variants and perform follow up analysis. I noticed that "jvarkit tview" has a "--readName" parameter which might meet my needs. However, it seems that neither "samtools view" nor "wally" can do that. I was wondering how I can use "jvarkit tview". Thank you very much

[lindenb]

you could you sam2tsv and check if there is a ALT variant carrying your variant. https://jvarkit.readthedocs.io/en/latest/Sam2Tsv/ or https://jvarkit.readthedocs.io/en/latest/Biostar322664/

[gudedsh]

Thank you.