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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.
The text was updated successfully, but these errors were encountered:
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.
The text was updated successfully, but these errors were encountered: