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This is the development version of ompBAM; for the stable release version, see ompBAM.

C++ Library for OpenMP-based multi-threaded sequential profiling of Binary Alignment Map (BAM) files

Bioconductor version: Development (3.19)

This packages provides C++ header files for developers wishing to create R packages that processes BAM files. ompBAM automates file access, memory management, and handling of multiple threads 'behind the scenes', so developers can focus on creating domain-specific functionality. The included vignette contains detailed documentation of this API, including quick-start instructions to create a new ompBAM-based package, and step-by-step explanation of the functionality behind the example packaged included within ompBAM.

Author: Alex Chit Hei Wong [aut, cre, cph]

Maintainer: Alex Chit Hei Wong <a.wong at centenary.org.au>

Citation (from within R, enter citation("ompBAM")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

ompBAM API Documentation HTML R Script
Reference Manual PDF


biocViews Alignment, DataImport, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.7.0
In Bioconductor since BioC 3.15 (R-4.2) (2 years)
License MIT + file LICENSE
Imports utils, Rcpp, zlibbioc
System Requirements
URL https://github.com/alexchwong/ompBAM
Bug Reports https://support.bioconductor.org/
See More
Suggests RcppProgress, knitr, rmarkdown, roxygen2, devtools, usethis, desc, testthat (>= 3.0.0)
Linking To
Depends On Me
Imports Me SpliceWiz
Suggests Me
Links To Me SpliceWiz
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package ompBAM_1.7.0.tar.gz
Windows Binary ompBAM_1.7.0.zip
macOS Binary (x86_64) ompBAM_1.7.0.tgz
macOS Binary (arm64) ompBAM_1.7.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ompBAM
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ompBAM
Bioc Package Browser https://code.bioconductor.org/browse/ompBAM/
Package Short Url https://bioconductor.org/packages/ompBAM/
Package Downloads Report Download Stats