Possible Types for INFO fields are: Integer, Float, Flag, Character, and String.
The Number entry is an Integer that describes the number of values that can be included with the INFO field.
For example, if the INFO field contains a single number, then this value should be 1;
if the INFO field describes a pair of numbers, then this value should be 2 and so on.
If the field has one value per alternate allele then this value should be 'A';
if the field has one value for each possible genotype (more relevant to the FORMAT tags) then this value should be 'G'.
If the number of possible values varies, is unknown, or is unbounded, then this value should be '.'.
The 'Flag' type indicates that the INFO field does not contain a Value entry, and hence the Number should
be 0 in this case. The Description value must be surrounded by double-quotes.
Double-quote character can be escaped with backslash (\") and backslash as \.
Hi Jeremy -
It crossed my mind that v4.1 might have been the issue for this one,
thanks for working on a fix!
bugs email@example.com 6-10
Could it somehow be related to this ticket (the second issue, the first
one I don't know about)? Seems unlikely since the bcf was created by
mpileup in Galaxy. I think the bcftools view tool might just have
another problem, or the input data is problematics (I can't figure out
what though), but am asking to double check.
One of the bug reports from the user about the problem in the ticket is
Anyway, will this go on Main soon? Did it already? I am restarting the
job from the first bug report to test, the wrapper is the same version
but I don't think that needs a change.
The second one I'm not sure about - that job eventually hits wall-time
out and errors if the problem still exists. So, just eats up resource.
I am looking through other recent bug reports that are unresolved to see
if any others are related - pretty sure this is the only one, but double
Thanks for the contribution Saket. IMO, we need to phase out usage of vcfpytools and move to simply wrapping vcftools. vcfpytools is very old and, as you and others have discovered, not compatible with newer versions of the VCF format. vcftools, OTOH, is under active development and driven by the 1000 genomes project.
Does anyone else feel strongly about either continuing to use vcfpytools or moving to vcftools?
I will merge this in. I also have two comments: (1) these changes should be pushed to the vcfpytools repository as well: https://github.com/AlistairNWard/vcfPytools and (2) the Galaxy project will be moving from vcfpytools to vcftools in the future for the reasons discussed previously.