Stitch FASTQ reads shredded with shred.sh from BBTools back together

stitch-fastq.jl

# tested on Julialang v.1.10.2 , DataStructures v0.18.16, and FASTX v2.1.4
# Usage
# $ julia stitch-fastq.jl chr20.herro.fasta.Q30.recal.shred.fastq > chr20.herro.fasta.Q30.recal.fastq
#
import Pkg; Pkg.add("FASTX")
import Pkg; Pkg.add("DataStructures")
using DataStructures
using FASTX

function process_fastq_file(filename::String)
    reader = FASTQReader(open(filename))
    sequencesS = Dict{String, String}()
    sequencesQ = Dict{String, String}()
    sequences1 = Dict{String, String}()
    sequences2 = Dict{String, String}()

    for record in reader
        # Get identifier
        main_id = string(identifier(record))
        seq = sequence(record)
        qual = quality(record)
        sequencesS[main_id] = seq
        sequencesQ[main_id] = qual
    end

    close(reader)
        
    sorted_pairs1 = OrderedDict(sort(collect(pairs(sequencesS))))
    sorted_pairs2 = OrderedDict(sort(collect(pairs(sequencesQ))))

    for (id, seq) in sorted_pairs1
        main_id = split(id, '_')[1]
        # Aggregate sequences by the main identifier
        if haskey(sequences1, main_id)
            sequences1[main_id] *= seq
        else
            sequences1[main_id] = seq
        end
    end

    for (id, qual) in sorted_pairs2
        main_id = split(id, '_')[1]
        # Aggregate sequences by the main identifier
        if haskey(sequences2, main_id)
            sequences2[main_id] *= qual
        else
            sequences2[main_id] = qual
        end
    end

    # Print the aggregated sequences
    for id in keys(sequences1)
        seq = sequences1[id]
        qual = sequences2[id]
        println("@$id")
        println(seq)
        println("+")
        println(qual)
    end
end

# Check if a filename is passed as a command line argument
if length(ARGS) < 1
    println("Usage: julia ", PROGRAM_FILE, " <filename.fastq>")
    return
end
# Example usage with command line argument
process_fastq_file(ARGS[1])