Introduction | Install and load the package | A quick overview of the functionality available in the package | Explode CIGAR strings | Tabulate CIGAR operations | Calculate the number of positions spanned by a CIGAR | Trim CIGAR strings along the reference or query space | Turn CIGAR strings into ranges of positions | Project positions from query to reference space and vice versa | Project sequences from one space to the other | Session information
Package: cigarillo 1.3.0
Hervé Pagès
cigarillo: Efficient manipulation of CIGAR strings
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.
Authors:
cigarillo_1.3.0.tar.gz
cigarillo_1.3.0.zip(r-4.7)cigarillo_1.3.0.zip(r-4.6)cigarillo_1.3.0.zip(r-4.5)
cigarillo_1.3.0.tgz(r-4.6-x86_64)cigarillo_1.3.0.tgz(r-4.6-arm64)cigarillo_1.3.0.tgz(r-4.5-x86_64)cigarillo_1.3.0.tgz(r-4.5-arm64)
cigarillo_1.3.0.tar.gz(r-4.7-arm64)cigarillo_1.3.0.tar.gz(r-4.7-x86_64)cigarillo_1.3.0.tar.gz(r-4.6-arm64)cigarillo_1.3.0.tar.gz(r-4.6-x86_64)
cigarillo_1.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
cigarillo/json (API)
| # Install 'cigarillo' in R: |
| install.packages('cigarillo', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/bioconductor/cigarillo/issues
On BioConductor:cigarillo-1.3.0(bioc 3.24)cigarillo-1.2.0(bioc 3.23)
infrastructurealignmentsequencematchingsequencingbioconductor-packagecore-package
Last updated from:df1f0466ac. Checks:9 NOTE, 2 OK, 3 WARNING. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 546 | ||
| linux-devel-arm64 | NOTE | 456 | ||
| linux-devel-x86_64 | NOTE | 566 | ||
| source / vignettes | OK | 595 | ||
| linux-release-arm64 | NOTE | 460 | ||
| linux-release-x86_64 | NOTE | 545 | ||
| macos-release-arm64 | NOTE | 148 | ||
| macos-release-x86_64 | NOTE | 368 | ||
| macos-oldrel-arm64 | NOTE | 142 | ||
| macos-oldrel-x86_64 | NOTE | 509 | ||
| windows-devel | WARNING | 526 | ||
| windows-release | WARNING | 458 | ||
| windows-oldrel | WARNING | 438 | ||
| wasm-release | OK | 251 |
Exports:cigar_extent_along_pwacigar_extent_along_querycigar_extent_along_refCIGAR_OPScigar_ops_visibilitycigars_as_ranges_along_pwacigars_as_ranges_along_querycigars_as_ranges_along_refcigars_as_RleListexplode_cigar_oplensexplode_cigar_opsfast_map_ref_ranges_to_querymap_ref_ranges_to_querynarrow_cigars_along_querynarrow_cigars_along_refproject_sequencesquery_pos_as_ref_posref_pos_as_query_postabulate_cigar_opstrim_cigars_along_querytrim_cigars_along_refvalidate_cigars
Dependencies:BiocGenericsBiostringscrayongenericsIRangesS4VectorsSeqinfoXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Efficient manipulation of CIGAR strings | cigarillo-package cigarillo |
| Calculate the number of positions spanned by a CIGAR string | cigar_extent cigar_extent_along_pwa cigar_extent_along_query cigar_extent_along_ref |
| Visibility of CIGAR operations | CIGAR_OPS cigar_ops_visibility |
| Turn CIGAR strings into ranges of positions | cigars_as_ranges cigars_as_ranges_along_pwa cigars_as_ranges_along_query cigars_as_ranges_along_ref |
| Explode CIGAR strings | cigars_as_RleList explode_cigars explode_cigar_oplens explode_cigar_ops validate_cigars |
| Map ranges relative to reference space to query space | fast_map_ref_ranges_to_query map_ref_ranges_to_query |
| Project positions from query to reference space and vice versa | project_positions query_pos_as_ref_pos ref_pos_as_query_pos |
| Project sequences from one space to the other | project_sequences |
| Tabulate CIGAR operations | tabulate_cigar_ops |
| Trim CIGAR strings along the reference or query space | narrow_cigars_along_query narrow_cigars_along_ref trim_cigars trim_cigars_along_query trim_cigars_along_ref |
