Replace the header from a .bam file — bam_reheader

This function replaces the header from one .bam file with a header from a different .sam file. This function mimics the function of the 'reheader' function in samtools. It is not intended for use by users.

Usage

bam_reheader_R(
  head,
  old_bam,
  new_bam = paste(tools::file_path_sans_ext(old_bam), "h.bam", sep = "")
)

Arguments

head: A file name and location for the .sam file with the new header.
old_bam: A file name and location for the .bam file which you would
new_bam: A file name for the new .bam file with a replaced header. Defaults to the same base filename plus 'h.bam'. For example, 'example.bam' will be written as 'exampleh.bam'.

Value

This function will return a new .bam file with a replaced header. The function also outputs the new .bam filename.