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# Bug description
Running SVIM on some long read PacBio bam files, I get an error from tabix, that the resulting sequences are unsorted.
```bash
[E::hts_idx_push] Unsorted positions on sequence #1:…
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> And another thought: do we prevent users from using a set, where the denominator is a subset of the numerator? In that case we should have values above 1. Do we have a guard there?
_Originally po…
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There seems to be a large KP.3.1.1+S:S31F branch, while KP.3.1.1 shall have S:31del.
That branch is driven by Denmark seqs which do not handle S:S31del well. When Querying C12616T, A13121T, C2165…
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The current `Alignment` struct for representing alignment results is defined as follows:
```rust
pub struct Alignment {
pub score: i32,
pub ystart: usize,
pub xstart: usize,
pu…
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The current definition of 'variant collection' in SO is “a sequence collection comprised of one or more sequences of an individual”.
A. It is not clear what is meant by ‘of an individual’ . . . this s…
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Wasm producers such as LLVM often generate Wasm code with a so-called shadow stack in order to handle parameters and return values that did not fit the Wasm function parameter and result passing model…
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Hi !
I used your pipeline ` pangenome-graph-from-assemblies` to construct a VCF file, but I noticed that some of the variants have an unusually high number of alleles. see belows:
`1 18300 .…
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regarding mutations_per_variant computation in build_variants.ipynb. There is a points I can't understand.
How can you have more than one variant that has 0 codon substitituions? If a sequence has …
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Hello,
I would like to use VarSim to generate synthetic reads for structural variants from a given ground truth VCF file. To achieve this, I am using VarSim with the following parameters:
```
var…