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arq5x / lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery
MIT License
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docs: specify whether output coordinates are 0 or 1 based #356

Open amcpherson opened 3 years ago

amcpherson commented 3 years ago

Apologies if this is already specified and i missed it

ryanlayer commented 3 years ago

We follow the spec. So the VCF is 1 based and the bEDPE is zero based.

On Fri, Apr 9, 2021 at 11:18 AM Andrew McPherson @.***> wrote:

Apologies if this is already specified and i missed it

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bartgrantham commented 9 months ago

Hi, I'm new to lumpy/smoove/CNV calling, and I believe I'm stumbling over a bug in lumpy that sometimes produces zeros for the position in vcfs. We're using version lumpy v0.2.13, which appears rather old but that is what is distributed with the smoove docker image. It's happening with 2 of 27473 variants called in my sample.

Downstream of lumpy something consumes that 0, subtracts 1, and writes 4294967296 (ie 32-bit MAXINT) as the position, which in turn throws a wrench into indexing the not-actually-sorted vcf.

Is this maybe a known bug that is fixed in more recent versions?

ryanlayer commented 9 months ago

That is not a know bug. Do you have any sense of where it subtracts 1?

On Thu, Oct 19, 2023 at 10:59 PM Bart Grantham @.***> wrote:

Hi, I'm new to lumpy/smoove/CNV calling, and I believe I'm stumbling over a bug in lumpy that sometimes produces zeros for the position in vcfs. We're using version lumpy v0.2.13, which appears rather old but that is what is distributed with the smoove docker image. It's happening with 2 of 27473 variants called in my sample.

Downstream of lumpy something consumes that 0, subtracts 1, and writes 4294967296 (ie 32-bit MAXINT) as the position, which in turn throws a wrench into indexing the not-actually-sorted vcf.

Is this maybe a known bug that is fixed in more recent versions?

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bartgrantham commented 8 months ago

I don't. I can look into what is causing it in a bit. I'm still wrapping my head around how these pieces fit together in smoove, once I have a better handle on it I'll do some debugging.