Invalid literal for int() with base 10: '.' about stranger HOT 3 CLOSED

Right, so this happens if for some reason TRGT does not set MC at all, only to a .. I'll make a simple workaround, but for the bigger picture, could you provide some info as to under what conditions this is happening? I have not yet seen it in an actual sample run? MC typically appears set to the reference repeat len if no deviating allele was found? Is it a "no call" when no allele had good enough quality? If so, we can just ignore it.

If its actual reference calls that happen for other reasons, we should perhaps parse the reference allele size from the repeat definitions and set it on the output. Or better yet, ask Egor and co to do so. 😊

from stranger.

Thank you. This example happens when there are no reads in the region.

from stranger.

Gotcha. Ok, that is not going to happen very often, and I guess 0 is a good a size guesstimate as any if there are no reads at all mapping. 😸

from stranger.