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Add SVStratify and GroupedSVCluster tools #8990

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Add SVStratify and GroupedSVCluster tools #8990

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Commits on Oct 2, 2024

  1. Require both overlap and breakend proximity for depth-only SV clustering 

     This is a combination of 2 commits.

Implement SVStratify

Interchrom events

Start unit tests

Finish unit tests

Multiple contexts per stratum

Integration tests; fix empty context bug

Test duplicate context name

Handle CPX/CTX, add some tests

Compiler error

Prioritize SR and PE evidence types for representative breakpoint strategy

Add SVStratifiedCluster

Integration tests for SVStratifiedClustering

Unused line

Spooled sorting in cluster tools

Start fixing JointGCNVSegmentation

Fix JointGCNVSegmentation integration test

Rename to GroupedSVCluster

Fix sorting bug

Comment

Use RD_CN for CNV sample overlap; improve testing

Documentation

Add comment about requiresOverlapAndProximity

Allow empty EVIDENCE list

Add STRAT INFO field

Representative breakpoint by variant quality

Handle BOTHSIDES_SUPPORT and HIGH_SR_BACKGROUND in variant collapsing

Add expected exception
    @mwalker174
    mwalker174 committed Oct 2, 2024
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  2. Add vcf splitting as an option

    @mwalker174
    mwalker174 committed Oct 2, 2024
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