R Observatory: Metrics for StructuralVariantAnnotation version 1.28.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

StructuralVariantAnnotation

Bioc current

Variant annotations for structural variants

v1.28.0 · Package record · software · GPL-3 + file LICENSE

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.9 · May 3, 2019

Current · Requires R 4.6

1.0 In 15 of 49 releases 3.23

Description

StructuralVariantAnnotation provides a framework for analysis of structural variants within the Bioconductor ecosystem. This package contains contains useful helper functions for dealing with structural variants in VCF format. The packages contains functions for parsing VCFs from a number of popular callers as well as functions for dealing with breakpoints involving two separate genomic loci encoded as GRanges objects.

Advisories

None published for Bioconductor

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

47 16 exported

Complexity

3.4 avg / 46 max

Call network

47 nodes / 49 edges

Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.

Call graph

Open call graph →

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Lowest coverage

Per-function coverage is not measured for this package yet.

How coverage is measured·How the call graph is built

Code

Structure

Lines of code

4,545

Files

71

Compiled share

0%

Has compiled src

No

Language breakdown

R 2,141 (47.1%)Tests 1,106 (24.3%)Docs 942 (20.7%)Vignettes 356 (7.8%)

API

Exported functions

20

Internal functions

31

Recent export changes

v3.9+10 breakendRanges, breakpointRanges, breakpointgr2bedpe +7 more

Testing

Has tests

Yes

Test-to-code ratio

0.52

testthat edition

–

Docs

Roxygen coverage

100%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

0%

Unsafe pattern score

0

Dep constraint coverage

0%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

4.1.0

System requirements

–

C++ standard

–

License

GPL-3 + file LICENSE

License flags

SPDX valid, OSI approved

History

Versions

15

First release

2019-05-02

Latest release

2026-04-28

Avg cadence

182 days

Cold removal rate

–

Dep drift

6

LOC over versions

Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.

Documentation

In the Bioconductor 3.23 release

READMEYes · 55 wordsVignettesYes · 1 · dynamicNEWSYes · 67% structuredCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 23 (1 internal)includes a package overview page
Examples that run: 100%11 run in a plain check
Exported functions with examples: 58%
Documented parameters: 91%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

Structural Variant Annotation Package HTML

How these are measured

Repository practices

Bioconductor git repository

Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.

2 practices detected in the Bioconductor git repository

Continuous integration (1)

Travis CI (config file)

Governance and community (1)

Code of conduct

How this is detected

Topics

Software › Infrastructure › DataImport

Software › Technology › Sequencing

Software › WorkflowStep › Annotation

Software › ResearchField › Genetics

Software › BiologicalQuestion › VariantAnnotation

Maintainer: Daniel Cameron

Available on

CRANr2uBioconductorautoCRANCOPR

Depended on by (4)

Bioconductor (4)

NUMTDetect RTDetect svaNUMT svaRetro

Suggested by (1)

shiny.gosling

People

Daniel Cameron author maintainer
Ruining Dong author

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("StructuralVariantAnnotation")

Format

Cameron, D., & Dong, R. (2026). StructuralVariantAnnotation: Variant annotations for structural variants (Version 1.28.0) [Computer software]. https://bioconductor.org/packages/StructuralVariantAnnotation

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for StructuralVariantAnnotation version 1.28.0 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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