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vgteam
tools for working with genome variation graphs
## Changelog Entry To be copied to the [draft changelog](https://github.com/vgteam/vg/wiki/Draft-Changelog) by merger: * vg now uses `libsnarls`, which brings along many of the vg-ecosystem libraries ## Description This PR will...
## Changelog Entry To be copied to the [draft changelog](https://github.com/vgteam/vg/wiki/Draft-Changelog) by merger: * Failed Gitlab Docker builds are detected more reliably ## Description We want to avoid cases like https://ucsc-ci.com/vgteam/vg/-/jobs/96240#L3013...
Hi I'm running vg version 1.34. I'm attempting to create a splice graph. I have a GTF file where the first column represents the paths in the graph across all...
@rlorigro needs snarls in his CMake project and doesn't want to link against vg. We need to adjust the existing SnarlManager to support the new handlegraph-based snarl API (since @xchang1's...
Apparently when we wrote the code for `vg chunk` haplotype tracing, we thought that all graphs would have one ID increment per node along whatever path we're using to define...
To reproduce: ``` wget http://public.gi.ucsc.edu/~hickey/chrOther.clip.gfa.gaffixed.vg vg validate chrOther.clip.gfa.gaffixed.vg graph: valid vg mod -O ./chrOther.clip.gfa.gaffixed.vg | vg validate - graph invalid: missing edge between 53612th step (296702:1) and 53613th step (296702:1)...
Hello, I installed the latest version of VG with Conda. The installation went well, but there was a problem typing vg -h FATAL: kernel too old Aborted (core dumped)
I constructed a graph, pruned the graph, then indexed it using the following commands: `vg construct -r example.fa -v example.vcf -m 32 > example.vg` `vg prune -r example.vg > example_pruned.vg`...
It's my understanding that when performing linear alignment of paired-end reads, people typically follow this workflow: (1) pre-process reads in FASTQ file (2) align reads to linear reference, generating a...
`vg` downloads the `hopscotch_map` repository at runtime. There is no immediately visible reason why this is necessary, and is also inconsistent with the approach of vendoring dependencies in submodules in...
