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inst 040000
man 040000
tests 040000
vignettes 040000
.Rbuildignore 100644 0 kb
.gitignore 100644 1 kb
DESCRIPTION 100644 1 kb
LICENSE 100644 1 kb
NAMESPACE 100644 0 kb
NEWS 100644 0 kb 100644 1 kb
# ompBAM C++ Library for OpenMP-based multi-threaded sequential profiling of Binary Alignment Map (BAM) files # Description Although various tools for multi-threaded BAM processing (samtools, sambamba) are available, currently there are none available to the R/Bioconductor environment. Parallelism in R is achieved using BiocParallel or related packages. Typical alternatives include processing multiple BAM files, each using a single core. Although easy to set up, memory-intensive applications limit such approaches. ompBAM is a header-only C++ library based on OpenMP, allowing developers to implement OpenMP-based parallelism for the sequential reading of BAM files. ompBAM makes it easy by handling all the parallel file-access and bgzf decompression, allowing developers to focus on multi-threaded handling of individual reads. ## Installation ### On current R (>= 4.0.0) * Development version from Github: ``` library("devtools") install_github("alexchwong/ompBAM", dependencies=TRUE, build_vignettes = TRUE) ``` ## Documentation Access the ompBAM-API-Docs via its included vignette. This includes: * How to set up a new package R-project, ready-to-compile with ompBAM, as well as a 'Hello World' equivalent example function of the 'idxstats' function to demonstrate ompBAM * A step-by-step guide of how the idxstats function implemented in the example code is constructed * Detailed documentation of the `pbam_in` and `pbam1_t` objects that comprise ompBAM. ``` browseVignettes("ompBAM") ```