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try: replace the varcall process

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This commit is contained in:
kuoi 2024-09-13 15:34:33 +10:00
parent 7729c2e6ff
commit 54bf6d9c72
1 changed files with 15 additions and 2 deletions
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17
RGBEPP.d
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@ -258,6 +258,17 @@ 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){
createDir(DirConsensus);
foreach (string file; parallel(ARG_L,1)) {
string baseName = getBaseName(file);
string inputBam = DirBam ~ "/" ~ baseName ~ ".bam";
string outputFasta = DirConsensus ~ "/" ~ baseName ~ ".fasta";
string [] cmdConsen1 = [PathSamtools, "consensus", "-f", "fasta", inputBam, "-o", outputFasta];
executeCommand(cmdConsen1);
}
}
void processCon(string[] ARG_G, string[] ARG_L, string ARG_R, int ARG_T, string DirMap, string DirVcf, string DirConsensus, string PathBcftools) { void processCon(string[] ARG_G, string[] ARG_L, string ARG_R, int ARG_T, string DirMap, string DirVcf, string DirConsensus, string PathBcftools) {
createDir(DirConsensus); createDir(DirConsensus);
@ -423,6 +434,7 @@ void main(string[] args) {
string DirBam = DirHome ~ "/03_bam"; string DirBam = DirHome ~ "/03_bam";
string DirVcf = DirHome ~ "/04_vcf"; string DirVcf = DirHome ~ "/04_vcf";
string DirConsensus = DirHome ~ "/05_consen"; string DirConsensus = DirHome ~ "/05_consen";
string DirConsensus1 = DirHome ~ "/05_consen1";
string DirAlign = DirHome ~ "/06_macse"; string DirAlign = DirHome ~ "/06_macse";
string DirTrim = DirHome ~ "/07_trimal"; string DirTrim = DirHome ~ "/07_trimal";
@ -560,13 +572,14 @@ void main(string[] args) {
if (ARG_F == "all" || ARG_F == "varcall") { if (ARG_F == "all" || ARG_F == "varcall") {
if(testFiles([PathBcftools])){ if(testFiles([PathBcftools])){
processVarCall(ARG_L, ARG_R, ARG_T, DirMap, DirBam, DirVcf, PathBcftools); //processVarCall(ARG_L, ARG_R, ARG_T, DirMap, DirBam, DirVcf, PathBcftools);
} }
} }
if (ARG_F == "all" || ARG_F == "consen") { if (ARG_F == "all" || ARG_F == "consen") {
if(testFiles([PathBcftools])){ if(testFiles([PathBcftools])){
processCon(ARG_G, ARG_L, ARG_R, ARG_T, DirMap, DirVcf, DirConsensus, PathBcftools); //processCon(ARG_G, ARG_L, ARG_R, ARG_T, DirMap, DirVcf, DirConsensus, PathBcftools);
processConSam(ARG_L, DirBam, DirConsensus, PathSamtools);
processCombFasta(ARG_G, ARG_L, DirConsensus); processCombFasta(ARG_G, ARG_L, DirConsensus);
} }
} }