Annotation challenges about vcfr HOT 1 CLOSED

Hello, you appear to have done something I have never tried. And I think we'll have to call it a bug. You do not appear to be using a sequence (FASTA file). This means my code doesn't have a reliable way to determine the length of your chromosome. My code tries to make a guess by selecting the greatest value from the VCF file. You have an annotation beyond the greatest position in your VCF and this throws the error you've reported. At this point I think we have several options.

1. You could use your reference. You used this to to call variants, so you must have something. This will allow the code to git the chromosome length from this sequence.

2. You can omit the offending annotations. Something like:

vcf <- read.vcfR('example.vcf')
len <- max(as.numeric(as.character(vcf@fix[,'POS'])))
gff <- read.table("example.gff", sep='\t', quote='')
gff2 <- gff[gff[,4] <= len,]
gff2 <- gff2[gff2[,5] <= len,]

This would remove some of your annotations, so its suboptimal. But it works.

3. You could try the devel branch from GitHub, if you're into that sort of thing. I've used your example to engineer my function so that it can handle this sort of thing. It will eventually end up on CRAN. But as of today is only at GitHub. Thank you for helping me improve vcfR!

I hope that helps!

from vcfr.