try: replace the varcall process
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1 changed files with 2 additions and 0 deletions
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RGBEPP.d
2
RGBEPP.d
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@ -259,6 +259,7 @@ void processVarCall(string[] ARG_L, string ARG_R, int ARG_T, string DirMap, stri
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}
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void processConSam(string[] ARG_L, string DirBam, string DirConsensus, string PathSamtools){
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writeln("Consensus::Start");
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createDir(DirConsensus);
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foreach (string file; parallel(ARG_L,1)) {
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string baseName = getBaseName(file);
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@ -267,6 +268,7 @@ void processConSam(string[] ARG_L, string DirBam, string DirConsensus, string Pa
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string [] cmdConsen1 = [PathSamtools, "consensus", "-f", "fasta", inputBam, "-o", outputFasta];
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executeCommand(cmdConsen1);
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}
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writeln("Consensus::End");
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}
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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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