The **futurize** package allows you to easily turn sequential code into parallel code by piping the sequential code to the `futurize()` function. Easy! # TL;DR ```r library(futurize) plan(multisession) library(Rsamtools) bv <- BamViews(bam_files) counts <- countBam(bv) |> futurize() ``` # Introduction This vignette demonstrates how to use this approach to parallelize the **[Rsamtools]** functions. The **[Rsamtools]** Bioconductor package provides an interface to BAM (Binary Alignment Map) files and other high-throughput sequencing data formats. Functions like `countBam()` and `scanBam()` can process multiple BAM files in parallel when called with a `BamViews` object, which distributes work across BAM files using `bplapply()`. ## Example: Counting reads across multiple BAM files in parallel The `countBam()` function counts the number of records in BAM files. When called with a `BamViews` object containing multiple BAM files, the counting can be parallelized: ```r library(Rsamtools) bam_files <- c("sample1.bam", "sample2.bam", "sample3.bam") bv <- BamViews(bam_files) counts <- countBam(bv) ``` Here `countBam()` processes BAM files sequentially, but we can easily make it process them in parallel by piping to `futurize()`: ```r library(futurize) counts <- countBam(bv) |> futurize() ``` This will distribute the BAM file processing across the available parallel workers, given that we have set up parallel workers, e.g. ```r plan(multisession) ``` The built-in `multisession` backend parallelizes on your local computer and works on all operating systems. There are [other parallel backends] to choose from, including alternatives to parallelize locally as well as distributed across remote machines, e.g. ```r plan(future.mirai::mirai_multisession) ``` and ```r plan(future.batchtools::batchtools_slurm) ``` # Supported Functions The following **Rsamtools** functions are supported by `futurize()`: * `countBam()` * `scanBam()` [Rsamtools]: https://bioconductor.org/packages/Rsamtools/ [other parallel backends]: https://www.futureverse.org/backends.html