R Observatory: Metrics for VCFArray version 1.28.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

VCFArray

Bioc current

Representing on-disk / remote VCF files as array-like objects

v1.28.0 · software · GPL-3

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

VCFArray extends the DelayedArray to represent VCF data entries as array-like objects with on-disk / remote VCF file as backend. Data entries from VCF files, including info fields, FORMAT fields, and the fixed columns (REF, ALT, QUAL, FILTER) could be converted into VCFArray instances with different dimensions.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

10 1 exported

Complexity

5 avg / 18 max

Call network

10 nodes / 9 edges

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

Call graph

Open call graph →

Loading call graph…

Lowest coverage

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

Code

Structure

Lines of code

990

Files

14

Compiled share

0%

Has compiled src

No

Language breakdown

R 481 (48.6%)Tests 101 (10.2%)Docs 156 (15.8%)Vignettes 252 (25.5%)

API

Exported functions

3

Internal functions

9

Recent export changes

v3.9+3 VCFArray, coerce, vcffile

Testing & CI

Has tests

Yes

Test-to-code ratio

0.21

testthat edition

–

CI present

No

CI type

[]

PR gated

No

Docs

Roxygen coverage

100%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

–

Unsafe pattern score

0

Dep constraint coverage

44.4%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

3.6

System requirements

–

C++ standard

–

License

GPL-3

License flags

SPDX valid, OSI approved

History

Versions

15

First release

2019-05-09

Latest release

2026-04-28

Avg cadence

182 days

Cold removal rate

–

Dep drift

0

LOC over versions

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

Documentation

READMEYes · 141 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 0% structuredCode of conductNoContributing guideNo

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

Topics

Software › Infrastructure

Software › Infrastructure › DataRepresentation

Software › Technology › Sequencing

Software › BiologicalQuestion › VariantAnnotation

Depended on by (1)

Bioconductor (1)

S4Cartographer

People

Qian Liu author maintainer
Martin Morgan author

At a glance

Version: 1.28.0
Category: software
License: GPL-3
Requires R: ≥ 4.6
Maintainer: Qian Liu
Entered: 3.9 · May 3, 2019
Current: 3.23 · Apr 29, 2026

Available on

CRAN r2u Bioconductor autoCRAN COPR

Dependencies

Depends

R (>= 3.6)methodsBiocGenericsBiocDelayedArray (>= 0.7.28)Bioc

Imports

toolsGenomicRangesBiocVariantAnnotation (>= 1.29.3)BiocGenomicFiles (>= 1.17.3)BiocS4Vectors (>= 0.19.19)BiocRsamtoolsBioc

Suggests

SeqArrayBiocBiocStyleBiocBiocManager testthat knitr rmarkdown

Source & history

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("VCFArray")

Format

Liu, Q., & Morgan, M. (2026). VCFArray: Representing on-disk / remote VCF files as array-like objects (Version 1.28.0) [Computer software]. https://bioconductor.org/packages/VCFArray

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 VCFArray version 1.28.0 [Data set]. HJJB, LLC. Data release v2026-08-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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