malacology/RGBEPP
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try: replace the varcall process

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This commit is contained in:
kuoi 2024-09-13 15:35:35 +10:00
parent 54bf6d9c72
commit 516ce17d13
1 changed files with 2 additions and 0 deletions
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RGBEPP.d
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@ -259,6 +259,7 @@ void processVarCall(string[] ARG_L, string ARG_R, int ARG_T, string DirMap, stri
}
void processConSam(string[] ARG_L, string DirBam, string DirConsensus, string PathSamtools){
writeln("Consensus::Start");
createDir(DirConsensus);
foreach (string file; parallel(ARG_L,1)) {
string baseName = getBaseName(file);
@ -267,6 +268,7 @@ void processConSam(string[] ARG_L, string DirBam, string DirConsensus, string Pa
string [] cmdConsen1 = [PathSamtools, "consensus", "-f", "fasta", inputBam, "-o", outputFasta];
executeCommand(cmdConsen1);
}
writeln("Consensus::End");
}
void processCon(string[] ARG_G, string[] ARG_L, string ARG_R, int ARG_T, string DirMap, string DirVcf, string DirConsensus, string PathBcftools) {