malacology/RGBEPP
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polish: rm useless func

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This commit is contained in:
kuoi 2024-09-18 17:09:00 +10:00
parent 9b18eb1777
commit 56c0293057
1 changed files with 0 additions and 18 deletions
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18
RGBEPP.d
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@ -315,23 +315,6 @@ 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");
string DirConTaxa = DirConsensus ~ "/" ~ "taxa";
createDir(DirConsensus);
createDir(DirConTaxa);
foreach (string file; parallel(ARG_L,1)) {
string baseName = getBaseName(file);
string inputBam = DirBam ~ "/" ~ baseName ~ ".bam";
string outputFasta = DirConTaxa ~ "/" ~ baseName ~ ".fasta";
string [] cmdConsen1 = [PathSamtools, "consensus", "-f", "fasta", inputBam, "-o", outputFasta];
executeCommand(cmdConsen1);
}
writeln("Consensus::End");
}
void processConDenovo(string[] ARG_G, string[] ARG_L, int ARG_T, string DirAssembly, string DirVcf, string DirConsensus, string PathBcftools) {
createDir(DirConsensus);
@ -672,7 +655,6 @@ void main(string[] args) {
if (ARG_F == "all" || ARG_F == "consen") {
if(testFiles([PathBcftools])){
//processCon(ARG_G, ARG_L, ARG_R, ARG_T, DirMap, DirVcf, DirConsensus, PathBcftools);
//processConSam(ARG_L, DirBam, DirConsensus, PathSamtools);
processConDenovo(ARG_G, ARG_L, ARG_T, DirAssembly, DirVcf, DirConsensus, PathBcftools);
processCombFasta(ARG_G, ARG_L, DirConsensus);
}