alabaster.files
Bioc currentWrappers to Save Common File Formats
Release Lineage
Entered 3.18 · Oct 25, 2023
Current · Requires R 4.6
Description
Save common bioinformatics file formats within the alabaster framework. This includes BAM, BED, VCF, bigWig, bigBed, FASTQ, FASTA and so on. We save and load additional metadata for each file, and we support linkage between each file and its corresponding index.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
77 45 exported
Complexity
1.6 avg / 9 max
Call network
77 nodes / 55 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
3,262
Files
66
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
45
Internal functions
32
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.45
testthat edition
–
CI present
No
CI type
[]
PR gated
No
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
50%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
6
First release
2023-10-24
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
2
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 100%
- Documented parameters
- 100%
- Return-value docs
- 92%
- References docs
- 0%
Topics
People
- Aaron Lun author maintainer