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 in
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See how to installReview the instructions the agent will receive before you install.
library(ompBAM)
# Create a new package template that compiles with ompBAM
pkg_path <- file.path(tempdir(), "MyPkg")
use_ompBAM(pkg_path)
# Retrieve the path to an example BAM file provided by the package
bam_path <- ompBAM::example_BAM("Unsorted")
Input: A destination directory path for the new package.
Output: A fully configured R package directory structure containing C++ templates and configuration files linked to ompBAM.
ompBAM to handle file access, BGZF decompression, and thread management.pbam_in and pbam1_t APIs).Rsamtools or GenomicAlignments instead.htslib directly as ompBAM is optimized for whole-file sequential reads.Rcpp and a C++ compiler supporting OpenMP (e.g., gcc or clang with OpenMP libraries).use_ompBAM): The directory path where the new package project will be created.devtools::document() on the newly created package to generate the NAMESPACE and export the R wrapper functions.#ifdef _OPENMP directive in C++ code to ensure compatibility with systems that do not have OpenMP installed (such as default macOS configurations).pbam1_t::realize() if you need to store reads in memory across multiple calls of pbam_in::fillReads(), as virtual reads point to temporary buffers.libomp via Homebrew (brew install libomp) and configure compiler flags.pbam1_t objects after calling fillReads() leads to segmentation faults. Fix: Call realize() on the pbam1_t object to copy the data into persistent memory.omp_get_max_threads().No reviews yet. Tell others what you thought.
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