cigarillo
Bioc currentEfficient manipulation of CIGAR strings
Release Lineage
Entered 3.22 · Oct 30, 2025
Current · Requires R 4.6
Description
CIGAR stands for Concise Idiosyncratic Gapped Alignment Report. CIGAR strings are found in the BAM files produced by most aligners and in the AIRR-formatted output produced by IgBLAST. The cigarillo package provides functions to parse and inspect CIGAR strings, trim them, turn them into ranges of positions relative to the "query space" or "reference space", and project positions or sequences from one space to the other. Note that these operations are low-level operations that the user rarely needs to perform directly. More typically, they are performed behind the scene by higher-level functionality implemented in other packages like Bioconductor packages GenomicAlignments and igblastr.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
76 21 exported
Complexity
2.9 avg / 13 max
Call network
76 nodes / 117 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
4,602
Files
50
Compiled share
38.5%
Has compiled src
Yes
Language breakdown
API
Exported functions
22
Internal functions
16
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.62
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
16.7%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
2
First release
2025-10-29
Latest release
2026-07-13
Avg cadence
257 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
- Examples that run
- 100%
- Documented parameters
- 78%
- Return-value docs
- 100%
- References docs
- 0%
Topics
Depended on by (2)
Bioconductor (1)
CRAN (1)
People
- Hervé Pagès author maintainer
- Patrick Aboyoun contributor
- Fedor Bezrukov contributor
- Michael Lawrence author
- Martin Morgan contributor
- Valerie Obenchain author