Package: cigarillo
Title: Efficient manipulation of CIGAR strings
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.
biocViews: Infrastructure, Alignment, SequenceMatching, Sequencing
URL: https://bioconductor.org/packages/cigarillo
BugReports: https://github.com/Bioconductor/cigarillo/issues
Version: 1.3.0
License: Artistic-2.0
Encoding: UTF-8
Authors@R: c(
	person("Hervé", "Pagès", role=c("aut", "cre"),
		email="hpages.on.github@gmail.com",
		comment=c(ORCID="0009-0002-8272-4522")),
	person("Valerie", "Obenchain", role="aut"),
	person("Michael", "Lawrence", role="aut",
		email="lawremi@gmail.com"),
	person("Patrick", "Aboyoun", role="ctb"),
	person("Fedor", "Bezrukov", role="ctb"),
	person("Martin", "Morgan", role="ctb"))
Depends: methods, BiocGenerics, S4Vectors (>= 0.47.2), IRanges,
        Biostrings
Imports: stats
LinkingTo: S4Vectors, IRanges
Suggests: Rsamtools, GenomicAlignments, RNAseqData.HNRNPC.bam.chr14,
        BSgenome.Hsapiens.UCSC.hg19, testthat, knitr, rmarkdown,
        BiocStyle
VignetteBuilder: knitr
Collate: utils.R cigar_ops_visibility.R explode_cigars.R
        tabulate_cigar_ops.R cigar_extent.R trim_cigars.R
        cigars_as_ranges.R project_positions.R project_sequences.R
        map_ref_ranges_to_query.R
Config/pak/sysreqs: zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 13:05:53 UTC
RemoteUrl: https://github.com/bioc/cigarillo
RemoteRef: HEAD
RemoteSha: df1f0466acbe21c278861c82da76c16c6d02a01a
NeedsCompilation: yes
Packaged: 2026-06-23 14:56:29 UTC; root
Author: Hervé Pagès [aut, cre] (ORCID: <https://orcid.org/0009-0002-8272-4522>),
  Valerie Obenchain [aut],
  Michael Lawrence [aut],
  Patrick Aboyoun [ctb],
  Fedor Bezrukov [ctb],
  Martin Morgan [ctb]
Maintainer: Hervé Pagès <hpages.on.github@gmail.com>