Convert BAM with modifications to tabix format

The modbam_to_tabix function takes a ModBamResult object and converts it into a tabix file format, which is efficient for indexing and querying large datasets.

Usage

modbam_to_tabix(x, out_file, mod_code = NanoMethViz::mod_code(x))

Arguments

x

the ModBamResult object.

out_file

the path of the output tabix.

mod_code

the modification code to use, defaults to 'm' for 5mC methylation.

Value

invisibly returns the name of the created tabix file.

Details

The possible tags for mod_code can be found at https://samtools.github.io/hts-specs/SAMtags.pdf under the 'Base modifications' section.

Examples

out_file <- paste0(tempfile(), ".tsv.bgz")
mbr <- ModBamResult(
    methy = ModBamFiles(
        samples = "sample1",
        paths = system.file("peg3.bam", package = "NanoMethViz",
        mustWork = FALSE)
    ),
    samples = data.frame(
        sample = "sample1",
        group = "group1"
    )
)

modbam_to_tabix(mbr, out_file)
#> ℹ Writing data to temporary file: /tmp/Rtmp6cPRDt/file1ca73cc2a459.tsv
#> ✔ Writing data to temporary file: /tmp/Rtmp6cPRDt/file1ca73cc2a459.tsv [7ms]
#> 
#> ℹ Converting data to TSV
#> ✔ Converting data to TSV [359ms]
#> 
#> ℹ Sorting data
#> ✔ Sorting data [30ms]
#> 
#> ℹ Compressing data
#> ℹ Moving data to final location: /tmp/Rtmp6cPRDt/file1ca77c2c458.tsv.bgz
#> ℹ Compressing data

#> ✔ Compressing data [28ms]
#> 
#> ℹ Tabix file created: /tmp/Rtmp6cPRDt/file1ca77c2c458.tsv.bgz
#> ✔ Tabix file created: /tmp/Rtmp6cPRDt/file1ca77c2c458.tsv.bgz [12ms]
#>