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 · 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.

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.

Code

Structure

Lines of code

4,545

Files

77

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 & CI

Has tests

Yes

Test-to-code ratio

0.52

testthat edition

–

CI present

Yes

CI type

["travis"]

PR gated

No

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

READMEYes · 55 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductYesContributing guideNo

Examples that run: 100%
Documented parameters: 91%
Return-value docs: 100%
References docs: 0%

Topics

Software › Infrastructure › DataImport

Software › Technology › Sequencing

Software › WorkflowStep › Annotation

Software › ResearchField › Genetics

Software › BiologicalQuestion › VariantAnnotation

Depended on by (5)

Bioconductor (5)

shiny.gosling svaNUMT svaRetro NUMTDetect RTDetect

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 is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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