malacology/RGBEPP
1
0
Fork 0
Code Issues Pull requests Projects Releases1 Packages Wiki Activity Actions

polish: avoid reference mismatch

Browse source
This commit is contained in:
kuoi 2025-01-12 01:07:16 +11:00
parent b62f6c7766
commit 5137357012
2 changed files with 2 additions and 2 deletions

2
RGBEPP.d
View file

@ -340,7 +340,7 @@ void processVarCallDenovo(string[] ARG_L, int ARG_T, string DirAssembly, string
// Variant calling using bcftools
string[] cmdPileup = [PathBcftools, "mpileup", "-Oz", "--threads", ARG_T.to!string, "-f", referFasta, inputBam];
string[] cmdVarCall = [PathBcftools, "call", "-mv", "-Oz", "--threads", ARG_T.to!string];
string[] cmdNorm = [PathBcftools, "norm", "--threads", ARG_T.to!string, "-f", referFasta, "-Oz"];
string[] cmdNorm = [PathBcftools, "norm", "--threads", ARG_T.to!string, "-f", referFasta, "--check-ref", "s", "-Oz"];
string[] cmdFilter = [PathBcftools, "filter", "--threads", ARG_T.to!string, "--IndelGap", "5", "-Oz", "-o", outputVcf];
executeCommandPipe([cmdPileup, cmdVarCall, cmdNorm, cmdFilter]);
}

2
RGBEPP_refmix.d
View file

@ -396,7 +396,7 @@ void processVarCall(string[] ARG_L, string ARG_R, int ARG_T, string DirMap, stri
// Variant calling using bcftools
string[] cmdPileup = [PathBcftools, "mpileup", "-Oz", "--threads", ARG_T.to!string, "-f", ARG_R_refer, inputBam];
string[] cmdVarCall = [PathBcftools, "call", "-mv", "-Oz", "--threads", ARG_T.to!string];
string[] cmdNorm = [PathBcftools, "norm", "--threads", ARG_T.to!string, "-f", ARG_R_refer, "-Oz"];
string[] cmdNorm = [PathBcftools, "norm", "--threads", ARG_T.to!string, "-f", ARG_R_refer, "--check-ref", "s", "-Oz"];
string[] cmdFilter = [PathBcftools, "filter", "--threads", ARG_T.to!string, "--IndelGap", "5", "-Oz", "-o", outputVcf];
executeCommandPipe([cmdPileup, cmdVarCall, cmdNorm, cmdFilter]);
}