Further improvements to SV Annotation

Now that we have the basics and have our head around SV annotation, maybe we can look at some other things, and compare them with what we have:

[Integration of transcriptomics and long-read
genomics prioritizes structural variants in rare
disease](https://www.medrxiv.org/content/10.1101/2024.03.22.24304565v1.full.pdf) - Medrxiv 2024

CADD-SV

* https://genome.cshlp.org/content/early/2022/02/23/gr.275995.121
* https://github.com/kircherlab/CADD-SV

SVAFotate

* [Annotation of structural variants with reported allele frequencies and related metrics from multiple datasets using SVAFotate](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-022-05008-y)
* https://github.com/fakedrtom/SVAFotate

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🤖 Written by Claude — AnnotSV has been moved out into its own issue: #1533. This issue remains the umbrella comparison ticket for the other SV annotation tools (CADD-SV, SVAFotate, ClassifyCNV, DeepSVP, etc.).

Start by reviewing the current SV annotation behavior and the linked CADD-SV, SVAFotate, and transcriptomics/long-read genomics resources; AnnotSV is tracked separately in issue #1533. The issue does not name files, tests, or a specific change, so the first step is to establish which tools and comparisons belong in scope and what completion means.

Written by the indexing model from the issue text.