gmapR
Bioc currentAn R interface to the GMAP/GSNAP/GSTRUCT suite
Release Lineage
Entered 2.9 · Nov 1, 2011
Current · Requires R 4.6
Description
GSNAP and GMAP are a pair of tools to align short-read data written by Tom Wu. This package provides convenience methods to work with GMAP and GSNAP from within R. In addition, it provides methods to tally alignment results on a per-nucleotide basis using the bam_tally tool.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
5190 14 exported
Complexity
2.2 avg / 24 max
Call network
5190 nodes / 10276 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
505,336
Files
588
Compiled share
99.2%
Has compiled src
Yes
Language breakdown
API
Exported functions
15
Internal functions
115
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
93.3%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
33.3%
Unsafe pattern score
0
Dep constraint coverage
52.9%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
2.15.0
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
30
First release
2011-10-31
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
19
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 15
- Examples that run
- 33%2 run in a plain check · 4 never run
- Exported functions with examples
- 42%
- Documented parameters
- 97%
- Return-value docs
- 25%
- Help pages citing references
- 0%
- gmapR PDF
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
No development-tooling practices detected in the Bioconductor git repository.
Topics
Depended on by (3)
Bioconductor (3)
Suggested by (2)
People (from the free-text Author field)
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("gmapR")Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.