polish: add get path from config file
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9ae0c38656
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391dc5c17d
1 changed files with 70 additions and 32 deletions
104
RGBEPP.d
104
RGBEPP.d
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@ -8,6 +8,7 @@ import std.conv;
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import std.array;
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import std.path;
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import std.parallelism;
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import std.regex;
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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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@ -107,10 +108,10 @@ string[] getARG_G(string ARG_R){
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return ARG_G;
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}
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void processQualityControl(string[] ARG_L, string DirRaw, string DirQcTrim, int ARG_T) {
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void processQualityControl(string[] ARG_L, int ARG_T, string DirRaw, string DirQcTrim, string PathFastp) {
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// Prepare directory
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createDir(DirQcTrim);
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writeln("QcTrimming::Start");
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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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@ -121,30 +122,30 @@ void processQualityControl(string[] ARG_L, string DirRaw, string DirQcTrim, int
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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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string[] cmdQcTrim = [PathFastp, "-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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executeCommand(cmdQcTrim);
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}
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writeln("QcTrimming::End");
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}
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}
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void processMapping(string ARG_R, string[] ARG_L, string DirQcTrim, string DirMap, int ARG_T) {
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void processMapping(string[] ARG_L, string ARG_R, int ARG_T, string DirQcTrim, string DirMap, string PathBowtie2, string PathSamtools) {
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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 PathBowtie2_build = PathBowtie2 ~ "-build";
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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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string[] cmdBuildDB = [PathBowtie2_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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@ -154,9 +155,9 @@ void processMapping(string ARG_R, string[] ARG_L, string DirQcTrim, string DirMa
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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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string[] cmdMap = [PathBowtie2, "-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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string[] cmdSam2Bam = [PathSamtools, "view", "-bS", "-@", ARG_T.to!string, "-o", outputBam];
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executeCommandPipe([cmdMap, cmdSam2Bam]);
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@ -164,7 +165,7 @@ void processMapping(string ARG_R, string[] ARG_L, string DirQcTrim, string DirMa
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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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void processPostMap(string[] ARG_L, int ARG_T, string DirMap, string DirBam, string PathSamtools) {
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createDir(DirBam);
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writeln("PostMapping::Start");
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@ -175,12 +176,12 @@ void processPostMap(string[] ARG_L, int ARG_T, string DirMap, string DirBam) {
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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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string[] cmdFixmate = [PathSamtools, "fixmate", "-@", ARG_T.to!string, "-m", inputBam, "-"];
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string[] cmdSort = [PathSamtools, "sort", "-@", ARG_T.to!string, "-"];
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string[] cmdMarkdup = [PathSamtools, "markdup", "-@", ARG_T.to!string, "-", outputBam];
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executeCommandPipe([cmdFixmate, cmdSort, cmdMarkdup]);
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string [] cmdIndexBam = ["samtools", "index", "-@", ARG_T.to!string, outputBam];
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string [] cmdIndexBam = [PathSamtools, "index", "-@", ARG_T.to!string, outputBam];
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executeCommand(cmdIndexBam);
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}
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@ -188,7 +189,7 @@ void processPostMap(string[] ARG_L, int ARG_T, string DirMap, string DirBam) {
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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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void processVarCall(string[] ARG_L, string ARG_R, int ARG_T, string DirMap, string DirBam, string DirVcf, string PathBcftools) {
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writeln("VarCalling::Start");
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string[] Refs = getRef(ARG_R, DirMap);
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@ -202,10 +203,10 @@ void processVarCall(string[] ARG_L, string ARG_R, int ARG_T, string DirBam, stri
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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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string[] cmdPileup = [PathBcftools, "mpileup", "-Oz", "--threads", ARG_T.to!string, "-f", ARG_R_refer, inputBam];
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string[] cmdVarCall = [PathBcftools, "call", "-mv", "-Oz", "--threads", ARG_T.to!string];
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string[] cmdNorm = [PathBcftools, "norm", "--threads", ARG_T.to!string, "-f", ARG_R_refer, "-Oz"];
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string[] cmdFilter = [PathBcftools, "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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@ -213,7 +214,7 @@ void processVarCall(string[] ARG_L, string ARG_R, int ARG_T, string DirBam, stri
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}
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void processCon(string[] ARG_L, string ARG_R, int ARG_T, string[] ARG_G, string DirVcf, string DirConsensus, string DirMap) {
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void processCon(string[] ARG_G, string[] ARG_L, string ARG_R, int ARG_T, string DirMap, string DirVcf, string DirConsensus, string PathBcftools) {
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createDir(DirConsensus);
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string DirConTaxa = DirConsensus ~ "/" ~ "taxa";
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@ -231,18 +232,18 @@ void processCon(string[] ARG_L, string ARG_R, int ARG_T, string[] ARG_G, string
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string outputFasta = DirConTaxa ~ "/" ~ baseName ~ ".fasta";
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// index vcf.gz
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string[] cmdIndexVcf = ["bcftools", "index", inputVcf];
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string[] cmdIndexVcf = [PathBcftools, "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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string[] cmdCon = [PathBcftools, "consensus", "-f", ARG_R, inputVcf, "-o", outputFasta];
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executeCommand(cmdCon);
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}
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// Recombine the sequences based on genes
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writeln("Consensus::End");
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}
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void processCombFasta(string[] ARG_L, string[] ARG_G, string DirConsensus) {
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void processCombFasta(string[] ARG_G, string[] ARG_L, string DirConsensus) {
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string DirConTaxa = DirConsensus ~ "/" ~ "taxa";
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string DirConGene = DirConsensus ~ "/" ~ "gene";
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@ -305,13 +306,28 @@ void processAlign(string[] ARG_G, string DirConsensus, string DirAlign, string P
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string inputFasta = DirConGene ~ "/" ~ gene ~ ".fasta";
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string outAA = DirAlignAA ~ "/" ~ gene ~ ".fasta";
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string outNT = DirAlignNT ~ "/" ~ gene ~ ".fasta";
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string[] cmd = ["java", "-jar", PathMacse, "-prog", "alignSequences", "-seq" , inputFasta, "-out_AA", outAA, "-out_NT", outNT ];
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executeCommand(cmd);
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string[] cmdAlign = ["java", "-jar", PathMacse, "-prog", "alignSequences", "-seq" , inputFasta, "-out_AA", outAA, "-out_NT", outNT ];
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executeCommand(cmdAlign);
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}
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writeln("Align::End");
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}
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string getValueFromConfig(string file, string key) {
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string content = readText(file);
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string value;
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auto regex = regex(key ~ r"\s*=\s*(.+)");
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foreach (line; content.splitter("\n")) {
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if (auto match = matchFirst(line, regex)) {
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value = match.captures[1];
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break;
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}
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}
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return value;
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}
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void main(string[] args) {
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string pkgver = "0.0.3";
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@ -325,17 +341,27 @@ void main(string[] args) {
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string DirConsensus = DirHome ~ "/05_consen";
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string DirAlign = DirHome ~ "/06_macse";
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string PathFastp = "/usr/bin/fastp";
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string PathBowtie2 = "/usr/bin/bowtie2";
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string PathSamtools = "/usr/bin/samtools";
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string PathBcftools = "/usr/bin/bcftools";
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string PathMacse = "/usr/share/java/macse.jar";
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string PathTrimal = "/usr/bin/trimal";
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int ARG_T = 8;
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string[] ARG_G;
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string[] ARG_L;
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string ARG_C;
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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 "-c", "--config":
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i++;
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ARG_C = args[i];
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break;
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case "-f", "--functions":
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i++;
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ARG_F = args[i];
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@ -377,27 +403,39 @@ void main(string[] args) {
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ARG_G = getARG_G(ARG_R);
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}
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// get pathXXX form config file
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if (ARG_C != ""){
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PathFastp = getValueFromConfig(ARG_C, "fastp");
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PathBowtie2 = getValueFromConfig(ARG_C, "bowtie2");
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PathSamtools = getValueFromConfig(ARG_C, "samtools");
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PathBcftools = getValueFromConfig(ARG_C, "bcftools");
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PathMacse = getValueFromConfig(ARG_C, "macse");
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PathTrimal = getValueFromConfig(ARG_C, "trimal");
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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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processQualityControl(ARG_L, DirRaw, DirQcTrim, ARG_T);
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processQualityControl(ARG_L, ARG_T, DirRaw, DirQcTrim, PathFastp);
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}
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if (ARG_F == "all" || ARG_F == "map") {
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processMapping(ARG_R, ARG_L, DirQcTrim, DirMap, ARG_T);
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processMapping(ARG_L, ARG_R, ARG_T, DirQcTrim, DirMap, PathBowtie2, PathSamtools);
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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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processPostMap(ARG_L, ARG_T, DirMap, DirBam, PathSamtools);
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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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processVarCall(ARG_L, ARG_R, ARG_T, DirMap, DirBam, DirVcf, PathBcftools);
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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, ARG_G, DirVcf, DirConsensus,DirMap);
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processCombFasta(ARG_L, ARG_G, DirConsensus);
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processCon(ARG_G, ARG_L, ARG_R, ARG_T, DirMap, DirVcf, DirConsensus, PathBcftools);
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processCombFasta(ARG_G, ARG_L, DirConsensus);
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}
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if (ARG_F == "all" || ARG_F == "align") {
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