malacology/RGBEPP
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polish: add some para check

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This commit is contained in:
kuoi 2024-12-08 18:08:00 +11:00
parent 1da143bdbc
commit 5cef63d839
1 changed files with 42 additions and 21 deletions
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61
RGBEPP.d
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@ -59,6 +59,14 @@ bool testFiles(string[] filePaths) {
return pass;
}
bool testString(string input) {
return input.length != 0;
}
bool testStringArray(string[] input) {
return !input.empty;
}
void createDir(string path) {
if (!exists(path)) {
mkdir(path);
@ -587,55 +595,68 @@ void main(string[] args) {
writeln("RGBEPP::Start");
// Perform steps based on provided function argument
if (ARG_F == "all" || ARG_F == "clean") {
if(testFiles([PathFastp])){
processQcTrim(ARG_L, ARG_T, DirRaw, DirQcTrim, PathFastp);
if(testFiles([PathFastp]) && testStringArray(ARG_L)){
processQcTrim(ARG_L, ARG_T, DirRaw, DirQcTrim, PathFastp); //ARG_L
} else {
throw new Exception("please confirm paramenters are correct");
}
}
if (ARG_F == "all" || ARG_F == "assembly") {
if(testFiles([PathSpades])){
processAssembly(ARG_L, ARG_M, ARG_T, DirQcTrim, DirAssembly, PathSpades);
if(testFiles([PathSpades]) && testStringArray(ARG_L)){
processAssembly(ARG_L, ARG_M, ARG_T, DirQcTrim, DirAssembly, PathSpades); //ARG_L
processAssemMv(ARG_L, DirAssembly);
} else {
throw new Exception("please confirm paramenters are correct");
}
}
if (ARG_F == "all" || ARG_F == "map") {
if(testFiles([PathBowtie2, PathDiamond, PathSamtools, PathSortDiamond])){
processMappingDenovo(ARG_L, ARG_R, ARG_T, DirQcTrim, DirAssembly, DirMap, PathBowtie2, PathDiamond, PathSamtools, PathSortDiamond);
if(testFiles([PathBowtie2, PathDiamond, PathSamtools, PathSortDiamond]) && testStringArray(ARG_L) && testString(ARG_R) ){
processMappingDenovo(ARG_L, ARG_R, ARG_T, DirQcTrim, DirAssembly, DirMap, PathBowtie2, PathDiamond, PathSamtools, PathSortDiamond); //ARG_L, ARG_R
} else {
throw new Exception("please confirm paramenters are correct");
}
}
if (ARG_F == "all" || ARG_F == "postmap") {
if(testFiles([PathSamtools])){
processPostMap(ARG_L, ARG_T, DirMap, DirBam, PathSamtools);
if(testFiles([PathSamtools]) && testStringArray(ARG_L) ){
processPostMap(ARG_L, ARG_T, DirMap, DirBam, PathSamtools); //ARG_L
} else {
throw new Exception("please confirm paramenters are correct");
}
}
if (ARG_F == "all" || ARG_F == "varcall") {
if(testFiles([PathBcftools])){
processVarCallDenovo(ARG_L, ARG_T, DirAssembly, DirMap, DirBam, DirVcf, PathBcftools);
if(testFiles([PathBcftools]) && testStringArray(ARG_L) ){
processVarCallDenovo(ARG_L, ARG_T, DirAssembly, DirMap, DirBam, DirVcf, PathBcftools); //ARG_L
} else {
throw new Exception("please confirm paramenters are correct");
}
}
if (ARG_F == "all" || ARG_F == "consen") {
if(testFiles([PathBcftools])){
processConDenovo(ARG_G, ARG_L, ARG_T, DirAssembly, DirVcf, DirConsensus, PathBcftools);
processCombFasta(ARG_G, ARG_L, DirConsensus);
if(testFiles([PathBcftools]) && testStringArray(ARG_L) && testStringArray(ARG_G) ){
processConDenovo(ARG_G, ARG_L, ARG_T, DirAssembly, DirVcf, DirConsensus, PathBcftools); //ARG_G ARG_L
processCombFasta(ARG_G, ARG_L, DirConsensus); //ARG_G ARG_L
} else {
throw new Exception("please confirm paramenters are correct");
}
}
if (ARG_F == "all" || ARG_F == "align") {
if(testFiles([PathMacse]) && testJava){
processAlign(ARG_G, DirConsensus, DirAlign, PathMacse);
if(testFiles([PathMacse]) && testJava && testStringArray(ARG_G)){
processAlign(ARG_G, DirConsensus, DirAlign, PathMacse); //ARG_G
} else {
throw new Exception("please confirm paramenters are correct");
}
}
if (ARG_F == "all" || ARG_F == "trim") {
if(testFiles([PathTrimal])){
processTrimming(ARG_G, DirAlign, DirTrim, PathDelstop, PathTrimal);
if(testFiles([PathTrimal]) && testStringArray(ARG_G) ){
processTrimming(ARG_G, DirAlign, DirTrim, PathDelstop, PathTrimal); //ARG_G
} else {
throw new Exception("please confirm paramenters are correct");
}
}