samtools_sort_index {FLAMES}R Documentation

Samtools Sort and Index

Description

Sort and index the given BAM file, using Rsamtools.

Usage

samtools_sort_index(bam_in, bam_out)

Arguments

bam_in

the file path to the BAM file to sort and index

bam_out

path to the output indexed BAM file.

Value

file path to the created BAM

Examples

temp_path <- tempfile()
bfc <- BiocFileCache::BiocFileCache(temp_path, ask = FALSE)
file_url <-
    "https://raw.githubusercontent.com/OliverVoogd/FLAMESData/master/data"
genome_bam <- paste0(temp_path, "/align2genome.bam")
file.rename(bfc[[names(BiocFileCache::bfcadd(bfc, "Genome BAM", paste(file_url, "align2genome.bam", sep = "/")))]], genome_bam)

samtools_sort_index(genome_bam, tempfile(fileext = ".bam"))

[Package FLAMES version 0.99.31 Index]