Overview | Read throughput on a single large BAM | End-to-end impact tracks the read fraction | A note on cores and fairness | Beyond reading: in-reader aggregation | Output is identical to the standard tools | Try it | Reproducing the full benchmarks | Session information
Package: BamScaleR 0.99.2
Chirag Parsania
BamScaleR: Bioconductor-Friendly Multithreaded BAM Processing
Multithreaded sequential BAM processing built on top of the ompBAM C++ engine. BamScaleR provides user-friendly BAM read and scan interfaces designed for compatibility with existing Bioconductor workflows.
Authors:
BamScaleR_0.99.2.tar.gz
BamScaleR_0.99.2.zip(r-4.7-x86_64)BamScaleR_0.99.2.zip(r-4.7-arm64)BamScaleR_0.99.2.zip(r-4.6-x86_64)BamScaleR_0.99.2.zip(r-4.6-arm64)BamScaleR_0.99.2.zip(r-4.5-x86_64)
BamScaleR_0.99.2.tgz(r-4.6-x86_64)BamScaleR_0.99.2.tgz(r-4.6-arm64)BamScaleR_0.99.2.tgz(r-4.5-x86_64)BamScaleR_0.99.2.tgz(r-4.5-arm64)
BamScaleR_0.99.2.tar.gz(r-4.7-arm64)BamScaleR_0.99.2.tar.gz(r-4.7-x86_64)BamScaleR_0.99.2.tar.gz(r-4.6-arm64)BamScaleR_0.99.2.tar.gz(r-4.6-x86_64)
BamScaleR_0.99.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
BamScaleR/json (API)
| # Install 'BamScaleR' in R: |
| install.packages('BamScaleR', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/cparsania/bamscaler/issues
Pkgdown/docs site:https://cparsania.github.io
Uses libs:
softwaredataimportsequencingcoveragealignmentqualitycontrolzlibcppopenmp
Last updated from:5918290c5d. Checks:14 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 152 | ||
| linux-devel-arm64 | NOTE | 266 | ||
| linux-devel-x86_64 | NOTE | 355 | ||
| source / vignettes | OK | 266 | ||
| linux-release-arm64 | NOTE | 266 | ||
| linux-release-x86_64 | NOTE | 338 | ||
| macos-release-arm64 | NOTE | 411 | ||
| macos-release-x86_64 | NOTE | 530 | ||
| macos-oldrel-arm64 | NOTE | 322 | ||
| macos-oldrel-x86_64 | NOTE | 397 | ||
| windows-devel-arm64 | NOTE | 454 | ||
| windows-devel-x86_64 | NOTE | 355 | ||
| windows-release-arm64 | NOTE | 337 | ||
| windows-release-x86_64 | NOTE | 307 | ||
| windows-oldrel-x86_64 | NOTE | 328 | ||
| wasm-release | OK | 137 |
Exports:bam_countbam_coveragebam_coverage_bigwigbam_readdecode_compact_qualdecode_compact_seqdecode_seqqual_compactfragment_sizesmapq_dist
Dependencies:askpassBHBiocGenericsBiocParallelBiostringsbitopscigarillocodetoolscpp11crayoncurlformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicRangeshttrIRangesjsonlitelambda.rmimeompBAMopensslR6RcppRhtslibRsamtoolsS4VectorsSeqinfosnowsysUCSC.utilsXVector
Benchmarking BamScaleR: reader throughput and end-to-end workflow impact
Last update: 2026-10-13
Started: 2026-04-20
Getting started with BamScaleR
Introduction | Installation | Basic usage | Metadata-oriented BAM access | Filtering with ScanBamParam | Alignment-object output | Sequence and quality extraction | Fast count summaries | Relationship to existing Bioconductor tools | Session information
Last update: 2026-10-06
Started: 2026-10-06
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Count BAM records with Bioconductor-compatible filtering | bam_count |
| Per-base coverage, aggregated in C++ | bam_coverage |
| Write per-base coverage to a bigWig, computed in C++ | bam_coverage_bigwig |
| Fast BAM reading with Bioconductor-compatible arguments | bam_read |
| Decode compact BamScaleR quality output | decode_compact_qual |
| Decode compact BamScaleR sequence output | decode_compact_seq |
| Decode compact 'seq' and 'qual' columns in BamScaleR output | decode_seqqual_compact |
| Fragment-size distribution, aggregated in C++ | fragment_sizes |
| Mapping-quality (MAPQ) distribution, aggregated in C++ | mapq_dist |
