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VG annotate can't add BED records across the junctions of circular genomes #1775
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You should try:
Note the change (.xg instead of .xz). |
@ekg that xz was a typo in the command in the issue, not when running it. The command fails with the correct xg file. |
Ok let me try to reproduce this. Did you share the whole dataset off thread?
…On Mon, Jul 9, 2018, 13:41 JervenBolleman ***@***.***> wrote:
Reopened #1775 <#1775>.
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@ekg the links to the dataset (vg file and bed file) are in the first comment of mine. You will just need to build your own xg index but that is quick. |
I found the cause of this error. E-coli is circler genome. If BED file includes the annotation that it crosses the start-and-end point of e-coli genomes, the position of the start point of that annotation is greater than that of the end point.
Since I am not sure |
It looks like we'll have to teach |
When a line which is
Even if the genome is circular, should we handle all |
We should know if the path is circular, and accept |
Please describe:
vg annotate a 126 pangenome e. coli graph using bed files from EnsemblGeneomes.
Have an humongous vg gam file
These are the xz compressed vg file and bed file.
Please reindex the vg file for xg locally.
vg file
bed file
vg version is static compiled vg 1.8.0
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