Caralyn Reisle

I ran it again and printed out the first entry of text_test. It is odd, it looks like its trying to run a batch of zero. Something must be wrong...

I gave this a try and ran into some namespace/path errors with the latest version (https://github.com/Raldir/FEVEROUS/pull/18). I am trying this again with the path fixes I put in the latest...

Sorry for the delay, This is the error message I get with the changes in main ``` [INFO] 2021-10-05 12:25:46,778 - __main__ - Start extracting cells from Tables... 0%| |...

Are you using a virtualenv? version conflicts happen quite often when using the system install. I would edit the following to $ export MAVIS_ALIGNER='bwa mem' $ export MAVIS_ALIGNER_REFERENCE=~/MAVIS/reference_inputs/hg19.fa $ git...

For the initial long read assembly integration tests Changes to MAVIS - incorporate option for long read assembler - choose "weird" reads in the evidence gathering step - assemble with...

@sarahdada what version of straglr were you using here?

Hi @arnavaz! Thanks for making this issue. I've taken a quick look at the tool. It looks like they use a non-standard VCF output (custom SVTYPEs ex `SVTYPE=INS:R`) which means...

The error is popping up because the argument parser thinks you mean svict as a filepath. The convert command only works with a known input type (see help menu output...

@arnavaz awesome! can you put the details for the event you manually converted here? I will use it as a template for writing the parser and adding it as a...

Hi Oh, Sorry for the slow response. > Q1. If I change reference or annotated files, can I visualize viral integrations? You will be able to visualize any fusion proteins...