bam_reheader_R | R Documentation |
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.
bam_reheader_R( head, old_bam, new_bam = paste(tools::file_path_sans_ext(old_bam), "h.bam", sep = "") )
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 like to reheader. |
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'. |
This function will return a new .bam file with a replaced header. The function also outputs the new .bam filename.
# refPath <- system.file("extdata","target.fasta", package = "MetaScope") # file.copy(from = refPath, to = file.path(".", "target.fasta")) # mk_subread_index('target.fasta', split = .02) # readPath <- system.file("extdata", "reads.fastq", package = "MetaScope") # Rsubread::align(index = "target_1", readfile1 = readPath, # output_file = "example1.bam") # Rsubread::align(index = "target_2", readfile1 = readPath, # output_file = "example2.bam") # bam_files <- c('example1.bam','example2.bam') # com_head <- combined_header(bam_files) # bam_reheader_R(com_head, 'example2.bam') ## Note that the following would be an equivalent command if samtools is installed # system2("samtools reheader header_tmp.sam example2.bam > example2h.bam")
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