get_fragments_length: Extract fragment length from a BAM file.
In TearsWillFall/DNAfrags: Filter DNA fragments in BAM files by length and location

get_fragments_length

R Documentation

Extract fragment length from a BAM file.

This function takes a BAM file as input and outputs the fragment length of all reads in a TXT file.

get_fragments_length(
  bin_path = "tools/samtools/samtools",
  bam = "",
  remove_unmapped = TRUE,
  verbose = FALSE,
  threads = 1
)

`bin_path`	Path to samtools executable. Default path tools/samtools/samtools.
`bam`	Path to BAM file.
`remove_unmapped`	Removes unmapped reads and/or mates. Only in BAM files. Default TRUE
`verbose`	Enables progress messages. Default False.
`threads`	Number of threads to use.