Vcf sanity check

[Cristianetaniguti]

• Avoid VCF sanity check function to return errors only in the terminal
• Add option to export viewpoly HIDECAN input from GWASpoly run
• Add VCF sanity check to filter tab -- this still has a bug because the VCF reading is inside a ObserveEvent, the user doesn't need to press the button to start the process. If the process takes time, user will press the button and the app may crash if the analysis start without the requirements.
• New button to export PCA values data as csv
• Working in progress to create arm64 docker image for BIGapp - amd64 is done

[alex-sandercock]

There were a few additional files that seem to require that the input VCF be compressed. I think it is OK to allow the user to use an uncompressed VCF if that was the intention.

[alex-sandercock]

Is this requiring that the VCF file be compressed for the analysis to run?

[alex-sandercock]

It should be OK to use a compressed or uncompressed file

[Cristianetaniguti]

Yes, both are allowed, but there was a bug with our example uncompressed VCF because it has less/equal 100 markers, the same/less amount than the subsetting for testing. Bug fixed.
The check will only break if the file has the .gz but it is not compressed or the opposite, or if it has non compatible compression (bz2 or .xz)

[alex-sandercock]

We should not prevent users from trying the analysis with large marker sets, but a warning is useful to let them know if could take a while.

• I assume that the change here would be to add "max_markers" to warning_if_false instead of error_if_false?

[Cristianetaniguti]

yes, this was the required change... done!

[alex-sandercock]

Is VCF being required to be compressed?

[Cristianetaniguti]

Nope.. see comment above

[alex-sandercock]

Looks good!