malacology/RGBEPP
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity Actions

try: replace the varcall process

Browse source
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
Show stats Download patch file Download diff file Expand all files Collapse all files

2
RGBEPP.d
View file

@ -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){ void processConSam(string[] ARG_L, string DirBam, string DirConsensus, string PathSamtools){
writeln("Consensus::Start");
createDir(DirConsensus); createDir(DirConsensus);
foreach (string file; parallel(ARG_L,1)) { foreach (string file; parallel(ARG_L,1)) {
string baseName = getBaseName(file); 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]; string [] cmdConsen1 = [PathSamtools, "consensus", "-f", "fasta", inputBam, "-o", outputFasta];
executeCommand(cmdConsen1); 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) { void processCon(string[] ARG_G, string[] ARG_L, string ARG_R, int ARG_T, string DirMap, string DirVcf, string DirConsensus, string PathBcftools) {