samtools_as_bam {FLAMES} | R Documentation

## Samtools as BAM

### Description

Produces a compressed binary BAM file from a text based SAM file, using Rsamtools.

### Usage

    samtools_as_bam(sam_in, bam_out)

### Arguments

`sam_in` | file path to the input SAM file
`bam_out` | file path to the output BAM file

### Value

file path to the output BAM file.

### Examples

    temp_path <- tempfile()
    bfc <- BiocFileCache::BiocFileCache(temp_path, ask = FALSE)
    file_url <-
        "https://raw.githubusercontent.com/OliverVoogd/FLAMESData/master/data"
    tmp_sam <- paste0(temp_path, "/tmp_sam.sam")
    file.rename(bfc[[names(BiocFileCache::bfcadd(bfc, "Temp SAM", paste(file_url, "tmp_sam.sam", sep = "/")))]], tmp_sam)

    samtools_as_bam(tmp_sam, tempfile(fileext = "bam"))

[Package FLAMES version 1.0.2 Index]