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: 1.2.1
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
git_url: https://git.bioconductor.org/packages/cigarillo
git_branch: RELEASE_3_23
git_last_commit: f6d2ae7
git_last_commit_date: 2026-07-13
Repository: Bioconductor 3.23
Date/Publication: 2026-07-14
NeedsCompilation: yes
Packaged: 2026-07-14 20:57:22 UTC; biocbuild
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>
Built: R 4.6.1; aarch64-unknown-linux-gnu; 'Wed, 05 Aug 2026 12:49:11 +0900'; unix
