From 513735701262dd41667e86a319cd4ea07cced5aa Mon Sep 17 00:00:00 2001
From: Guoyi Zhang <kuoi@bioarchlinux.org>
Date: Sun, 12 Jan 2025 01:07:16 +1100
Subject: [PATCH] polish: avoid reference mismatch
---
RGBEPP.d | 2 +-
RGBEPP_refmix.d | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/RGBEPP.d b/RGBEPP.d
index 54da3d4..9aab996 100644
--- a/RGBEPP.d
+++ b/RGBEPP.d
@@ -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]);
}
diff --git a/RGBEPP_refmix.d b/RGBEPP_refmix.d
index e13dc63..b1636f1 100644
--- a/RGBEPP_refmix.d
+++ b/RGBEPP_refmix.d
@@ -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]);
}