bioconductor-cigarillo
Efficient manipulation of CIGAR strings
Efficient manipulation of CIGAR strings
To install this package, run one of the following:
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.
Summary
Efficient manipulation of CIGAR strings
Last Updated
Feb 26, 2026 at 13:47
License
Artistic-2.0
Supported Platforms