Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Rare clusters have all "n"s in 4th field, causing R to fail #23

Open
tedsharpe opened this issue Feb 22, 2022 · 0 comments
Open

Rare clusters have all "n"s in 4th field, causing R to fail #23

tedsharpe opened this issue Feb 22, 2022 · 0 comments

Comments

@tedsharpe
Copy link

Of the 359,984 clusters produced by processing the 1000 genomes cram for sample HG00150, 5 have nothing but "n" calls in the 4th field. Here are two examples:
chr1:24599821 left 7 nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn ccccccccccccccccccttcgttaacgacgctattaccaactaaa
chr2:232427156 left 5 nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn ttttttttttttttttttttttttttttttttttttctctccccccccccccccccctctccctttcttgtgtttttttttttttttttttttccgcctcccccccacctcccaggtt

When the R script attempts find deletions using such a cluster, the analysis fails with this error:
Error in width(strings) : NAs in 'x' are not supported
Calls: do.dels ... .charToXStringSet -> solveUserSEW -> width -> width

My workaround is to clean the cluster file of these few bad guys before processing, but perhaps do.dels.R could exclude them.

Thanks for the software.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant