polish: give a D version
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1 changed files with 318 additions and 0 deletions
318
RGBEPP.d
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318
RGBEPP.d
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#!/usr/bin/env rdmd
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import std.stdio;
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import std.file;
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import std.process;
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import std.algorithm;
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import std.conv;
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import std.array;
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import std.path;
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void show_help(string pkgver) {
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writeln("\t\t\t\t\t\033[0;47;31mR\033[0m\033[0;47;92mG\033[0m\033[0;47;94mB\033[0m\033[0;47m \033[0m\033[0;47;33mE\033[0m\033[0;47;94mP\033[0m\033[0;47;33mP\033[0m
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\t\t\tReference Genome based Exon Phylogeny Pipeline
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Version: ", pkgver, "
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License: GPL-2.0-only
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Author: Guoyi Zhang
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-c\t--contigs\tcontigs type: scaffolds or contigs
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-g\t--genes\t\tgene file path
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-f\t--functions\tfunctions type (optional): all clean map postmap varcall consen
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-h\t--help\t\tshow this information
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-l\t--list\t\tlist file path
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-m\t--memory\tmemory settings (optional, default 16 GB)
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-r\t--reference\treference genome path
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-t\t--threads\tthreads setting (optional, default 8 threads)
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--macse\t\tMacse jarfile path
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for example: ./your_program -c scaffolds -f all -l list -g genes \\
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-r reference.fasta \n");
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}
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void createDir(string path) {
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if (!exists(path)) {
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mkdir(path);
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}
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}
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void executeCommand(string[] cmd, string workingDir = "") {
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auto process = spawnProcess(cmd);
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if (wait(process) != 0) {
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writeln("Error executing command: ", cmd.join(" "));
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}
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}
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void executeCommandPipe(string[][] cmds) {
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Pid[] pids;
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scope(exit) {
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foreach (pid; pids) {
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wait(pid);
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}
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}
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// pipe init
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auto temp_pipe = pipe();
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// process first
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pids ~= spawnProcess(cmds[0], stdin, temp_pipe.writeEnd);
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// process cmd2 ~ cmdN-1
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for (int i = 1; i < cmds.length - 1; i++) {
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auto new_pipe = pipe(); // create next pipe
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pids ~= spawnProcess(cmds[i], temp_pipe.readEnd, new_pipe.writeEnd);
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temp_pipe = new_pipe; // update the pipe
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}
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// process final, output to stdout
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pids ~= spawnProcess(cmds[$-1], temp_pipe.readEnd, stdout);
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}
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string[] readArrFromFile(string filename) {
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string[] arr;
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try {
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arr = filename.readText().splitter.array;
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} catch (FileException ex) {
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writeln("Error reading file: ", ex.msg);
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} catch (Exception ex) {
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writeln("Exception: ", ex.msg);
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}
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return arr;
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}
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string getBaseName(string ARG_R){
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string ARG_R_extension = extension(ARG_R); // get extension
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string baseNameRef = baseName(ARG_R, ARG_R_extension); //rm dir and extension
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return baseNameRef;
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}
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string[] getRef(string ARG_R, string DirMap){
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string baseNameRef = getBaseName(ARG_R);
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string ARG_R_index = DirMap ~ "/index/" ~ baseNameRef; // bt2_index_base
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string ARG_R_refer = ARG_R_index ~ ".fasta"; //reference_in fasta file
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string[] Refs = [ARG_R_index, ARG_R_refer];
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return Refs;
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}
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void performQualityControl(string[] ARG_L, string DirRaw, string DirQcTrim, int ARG_T) {
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// Prepare directory
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createDir(DirQcTrim);
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foreach (string file; ARG_L) {
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string baseName = getBaseName(file);
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string inputFileR1 = DirRaw ~ "/" ~ baseName ~ "_R1.fastq.gz";
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string inputFileR2 = DirRaw ~ "/" ~ baseName ~ "_R2.fastq.gz";
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string outputFileR1 = DirQcTrim ~ "/" ~ baseName ~ "_R1.fastq.gz";
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string outputFileR2 = DirQcTrim ~ "/" ~ baseName ~ "_R2.fastq.gz";
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string jsonFile = DirQcTrim ~ "/" ~ baseName ~ ".json";
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string htmlFile = DirQcTrim ~ "/" ~ baseName ~ ".html";
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// Perform quality control and trimming using external program `fastp`
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string[] cmd = ["fastp", "-i", inputFileR1, "-I", inputFileR2,
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"-o", outputFileR1, "-O", outputFileR2,
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"-j", jsonFile, "-h", htmlFile,
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"-w", ARG_T.to!string];
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executeCommand(cmd);
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}
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}
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void performMapping(string ARG_R, string[] ARG_L, string DirQcTrim, string DirMap, int ARG_T) {
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writeln("Mapping::Start");
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// Prepare directory
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createDir(DirMap);
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createDir(DirMap ~ "/index");
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string[] Refs = getRef(ARG_R, DirMap);
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string ARG_R_index = Refs[0]; // bt2_index_base
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string ARG_R_refer = Refs[1]; //reference_in fasta file
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copy(ARG_R, ARG_R_refer);
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string[] cmdBuildDB = ["bowtie2-build", "--threads", ARG_T.to!string, ARG_R_refer, ARG_R_index];
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executeCommand(cmdBuildDB);
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foreach (string file; ARG_L) {
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string baseName = baseName(file, ".fastq.gz");
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string outputBam = DirMap ~ "/" ~ baseName ~ ".bam";
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string inputFileR1 = DirQcTrim ~ "/" ~ baseName ~ "_R1.fastq.gz";
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string inputFileR2 = DirQcTrim ~ "/" ~ baseName ~ "_R2.fastq.gz";
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// Perform mapping using Bowtie2 and converted to Bam using samtools
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string[] cmdMap = ["bowtie2", "-x", ARG_R_index, "-1", inputFileR1, "-2", inputFileR2,
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"-p", ARG_T.to!string];
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string[] cmdSam2Bam = ["samtools", "view", "-bS", "-@", ARG_T.to!string, "-o", outputBam];
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executeCommandPipe([cmdMap, cmdSam2Bam]);
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}
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writeln("Mapping::End");
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}
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void processPostMap(string[] ARG_L, int ARG_T, string DirMap, string DirBam) {
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createDir(DirBam);
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writeln("PostMapping::Start");
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foreach (string file; ARG_L) {
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string baseName = getBaseName(file);
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string inputBam = DirMap ~ "/" ~ baseName ~ ".bam";
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string outputBam = DirBam ~ "/" ~ baseName ~ ".bam";
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// Convert SAM to BAM, sort and remove duplicates using Samtools
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string[] cmdFixmate = ["samtools", "fixmate", "-@", ARG_T.to!string, "-m", inputBam, "-"];
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string[] cmdSort = ["samtools", "sort", "-@", ARG_T.to!string, "-"];
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string[] cmdMarkdup = ["samtools", "markdup", "-@", ARG_T.to!string, "-", outputBam];
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executeCommandPipe([cmdFixmate, cmdSort, cmdMarkdup]);
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}
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writeln("PostMapping::End");
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}
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void processIndexBam(string[] ARG_L, int ARG_T, string DirBam){
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writeln("Indexing::Start");
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//samtools index bam after markdup
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foreach (string file; ARG_L) {
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string baseName = getBaseName(file);
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string inputBam = DirBam ~ "/" ~ baseName ~ ".bam";
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string [] cmdIndexBam = ["samtools", "index", "-@", ARG_T.to!string, inputBam];
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executeCommand(cmdIndexBam);
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}
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writeln("Indexing::End");
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}
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void processVarCall(string[] ARG_L, string ARG_R, int ARG_T, string DirBam, string DirVcf, string DirMap) {
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writeln("VarCalling::Start");
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string[] Refs = getRef(ARG_R, DirMap);
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string ARG_R_refer = Refs[1]; //reference_in fasta file
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createDir(DirVcf);
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foreach (string file; ARG_L) {
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string baseName = getBaseName(file);
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string inputBam = DirBam ~ "/" ~ baseName ~ ".bam";
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string outputVcf = DirVcf ~ "/" ~ baseName ~ ".vcf.gz";
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// Variant calling using bcftools
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string[] cmdPileup = ["bcftools", "mpileup", "-Oz", "--threads", ARG_T.to!string, "-f", ARG_R_refer, inputBam];
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string[] cmdVarCall = ["bcftools", "call", "-mv", "-Oz", "--threads", ARG_T.to!string];
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string[] cmdNorm = ["bcftools", "norm", "--threads", ARG_T.to!string, "-f", ARG_R_refer, "-Oz"];
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string[] cmdFilter = ["bcftools", "filter", "--threads", ARG_T.to!string, "--IndelGap", "5", "-Oz", "-o", outputVcf];
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executeCommandPipe([cmdPileup, cmdVarCall, cmdNorm, cmdFilter]);
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}
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writeln("VarCalling::End");
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}
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void processCon(string[] ARG_L, string ARG_R, int ARG_T, string DirVcf, string DirConsensus, string DirMap) {
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createDir(DirConsensus);
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string[] Refs = getRef(ARG_R, DirMap);
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string ARG_R_refer = Refs[1]; //reference_in fasta file
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foreach (string file; ARG_L) {
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string baseName = getBaseName(file);
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string inputVcf = DirVcf ~ "/" ~ baseName ~ ".vcf.gz";
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string outputFasta = DirConsensus ~ "/" ~ baseName ~ ".fasta";
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// index vcf.gz
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string[] cmdIndexVcf = ["bcftools", "index", inputVcf];
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executeCommand(cmdIndexVcf);
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// Generate consensus sequences using bcftools
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string[] cmdCon = ["bcftools", "consensus", "-f", ARG_R, inputVcf, "-o", outputFasta];
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executeCommand(cmdCon);
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}
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}
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void main(string[] args) {
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string pkgver = "0.0.2";
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string DirHome = std.file.getcwd();
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string DirRaw = DirHome ~ "/00_raw";
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string DirQcTrim = DirHome ~ "/01_fastp";
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string DirMap = DirHome ~ "/02_bowtie2";
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string DirBam = DirHome ~ "/03_bam";
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string DirVcf = DirHome ~ "/04_vcf";
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string DirConsensus = DirHome ~ "/05_consen";
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string DirAlign = DirHome ~ "/06_macse";
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string PathMacse = "/usr/share/java/macse.jar";
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int ARG_T = 8;
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string[] ARG_L;
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string ARG_F;
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string ARG_R;
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if (args.length > 1){
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foreach (int i; 0 .. cast(int)args.length) {
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switch (args[i]) {
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case "-f", "--functions":
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i++;
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ARG_F = args[i];
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break;
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case "-h", "--help":
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show_help(pkgver);
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return;
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case "-l", "--list":
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i++;
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ARG_L ~= readArrFromFile( DirHome ~ "/" ~ args[i]);
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break;
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case "-r", "--reference":
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i++;
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ARG_R = args[i];
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break;
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case "-t", "--threads":
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i++;
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ARG_T = args[i].to!int;
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break;
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case "--macse":
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i++;
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PathMacse = args[i];
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break;
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default:
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break;
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}
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}
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} else {
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show_help(pkgver);
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return;
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}
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writeln("RGBEPP::Start");
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// Perform steps based on provided function argument
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if (ARG_F == "all" || ARG_F == "clean") {
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performQualityControl(ARG_L, DirRaw, DirQcTrim, ARG_T);
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}
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if (ARG_F == "all" || ARG_F == "map") {
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performMapping(ARG_R, ARG_L, DirQcTrim, DirMap, ARG_T);
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}
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if (ARG_F == "all" || ARG_F == "postmap") {
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processPostMap(ARG_L, ARG_T, DirMap, DirBam);
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}
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if (ARG_F == "all" || ARG_F == "indexbam") {
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processIndexBam(ARG_L, ARG_T, DirBam);
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}
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if (ARG_F == "all" || ARG_F == "varcall") {
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processVarCall(ARG_L, ARG_R, ARG_T, DirBam, DirVcf, DirMap);
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}
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if (ARG_F == "all" || ARG_F == "consen") {
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processCon(ARG_L, ARG_R, ARG_T, DirVcf, DirConsensus,DirMap);
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}
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writeln("RGBEPP::End");
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}
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