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(GenomicAlignments) se <- summarizeOverlaps(features, bam_files) |> futurize() ``` # Introduction This vignette demonstrates how to use this approach to parallelize the **[GenomicAlignments]** functions. The **[GenomicAlignments]** Bioconductor package provides efficient representation and manipulation of short genomic alignments. The `summarizeOverlaps()` function counts the number of reads that map to each feature (e.g. gene or exon) from one or more BAM files. When called with a `BamFileList`, the work is distributed across BAM files using `bplapply()`, which can be parallelized. ## Example: Running summarizeOverlaps() in parallel The `summarizeOverlaps()` function counts reads overlapping genomic features across multiple BAM files: ```r library(GenomicAlignments) library(Rsamtools) bam_files <- BamFileList(c("sample1.bam", "sample2.bam", "sample3.bam")) features <- GRanges("chr1", IRanges(start = c(1, 1000, 2000), end = c(500, 1500, 2500)) ) se <- summarizeOverlaps(features, bam_files) ``` Here `summarizeOverlaps()` processes BAM files sequentially, but we can easily make it process them in parallel by piping to `futurize()`: ```r library(futurize) se <- summarizeOverlaps(features, bam_files) |> 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 **GenomicAlignments** functions are supported by `futurize()`: * `summarizeOverlaps()` [GenomicAlignments]: https://bioconductor.org/packages/GenomicAlignments/ [other parallel backends]: https://www.futureverse.org/backends.html