Converts quality scores in BAM alignments to a single ASCII Phred Score you desire

changeBAMquality.jl

# note: outputs to STDOUT a SAM file without a header
# note2: remove auxillary tags and information
# note3: ignores RNEXT and PNEXT from BAM file (puts * and 0 respectivelv)
# tested with julialang v1.10.2 and XAM v0.4.0
# $ julia changeBAMquality.jl input.bam ? > test.sam.noheader
#
# to add a header from the original BAM file that had its qualities changed
# and add on a PG line
# $ ASCII_CHARACTER="?"
# $ INPUT=input.bam
# $ INPUT2=test.sam.noheader
# this is the command to make the BAM file
# $ cat <(samtools view -H $INPUT) <(echo -e "@PG\tID:changeBAMquality\tPN:changeBAMquality.jl\tVN:0.01\tCL:julia changeBAMquality.jl $INPUT $ASCII_CHARACTER") $INPUT2 |samtools view -Sb > test.bam
#
using XAM
using Base.Iterators: partition
using ArgParse

function parse_commandline()
    s = ArgParseSettings()

    @add_arg_table s begin
        "input_file"
            help = "Path to the input BAM file"
            required = true
        "ASCII_character"
            help = "ASCII character quality value to change, for examle ? for Q30"
            required = true
            arg_type = String
    end

    return parse_args(s)
end

function change_quality(input_file::String, ASCII_character::String)
    reader = open(BAM.Reader, input_file)
    record = BAM.Record()
    while !eof(reader)
        empty!(record)
        read!(reader, record)
        if BAM.ismapped(record)
            if BAM.isprimaryalignment(record)
                 println(BAM.tempname(record), "\t", BAM.flags(record), "\t", BAM.refname(record), "\t", BAM.position(record), "\t", BAM.mappingquality(record), "\t", BAM.cigar(record), "\t*", "\t0\t", BAM.templength(record), "\t", BAM.sequence(record), "\t", repeat(ASCII_character, BAM.seqlength(record)))
            end
        end
    end
    close(reader)
end



function main()
    parsed_args = parse_commandline()
    input_file = parsed_args["input_file"]
    ASCII_character = parsed_args["ASCII_character"]

    if length(ASCII_character) != 1
        println("Error: Input must be a single character.")
        return
    end

    if !isascii(ASCII_character[1])
        println("Error: Input must be an ASCII character.")
        return
    end

    change_quality(input_file, ASCII_character)
end

main()