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Optionally emit SV lengths #504

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yfarjoun
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@yfarjoun yfarjoun commented Aug 13, 2024

closes #503

This PR adds a commandline argument that emits the lengths of the SVs found on the reads into the VCF record that contains the resulting SV. The argument is suppressed (not showing in the "help") and is prefixed with dev- to indicate that it's a development/debugging option.

The only change to the output is the (currently non-optional) addition of the SVLENGTHS header line in the VCF. However, I'm happy to make this also optional. otherwise, the algorithm and output are unchanged unless --dev-emit-sv-lengths is provided on the command-line.

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yfarjoun commented Sep 9, 2024

I'd love to know what needs to be done to get some traction on this PR. It doesn't change the default behaviour, but it allows users to better understand the distribution of svlengths that the call have and thus perform better clustering and other downstream analyses.

Please do consider these changes and let me know if there's anything I can do to make it easier for the maintainers.

@fritzsedlazeck
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Thanks @hermannromanek could you take a look?

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Allow the optional emission of sv length of evidence
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