dsygu filter broken for non-translocations

[kdm9]

Hello,

I think some recent refactoring of filter_normal.py has broken dysgu filter. I suspect the cause is that process_intra() never returns None. From a brief inspection of dysgu filter --keep-all it seems to complain about low support for all non-TRA events. I tried to track the logic of process_intra() but ran out of time.

I've confirmed that version 1.6.2 works as expected, but nothing since then does, so I suspect the bug is somewhere here.

I've already made a PR for a bug that prevented using --keep-all since v1.6.2, #99.

best,
K

[kcleal]

Hi @kdm9,
Thanks for raising this, I will get this fixed asap.
Would you be able to share details of how you run used dysgu run/call + filter commands, and what read-type you are working with (Illumina, nanopore etc ..) Thanks!

[kdm9]

many thanks @kcleal, I've reached out by email to provide these details.

[kcleal]

v1.6.6 has been released - I think the issue should be resolved, but let me know if it still exists. v1.6.6 is on once, but not yet on Pypi.

[kdm9]

Just confirming that in our hands, dysgu filter is working again now