From 8498da5320686b7585a5223dcec6bebd8a3ba56f Mon Sep 17 00:00:00 2001 From: Ketian Yu Date: Tue, 17 Aug 2021 16:46:11 -0400 Subject: [PATCH] Change LDS format from string to number, change delimiter for LDS from vertical slash to comma --- src/Analysis.cpp | 2 +- src/DosageData.cpp | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/Analysis.cpp b/src/Analysis.cpp index ded6b03..18b4acb 100644 --- a/src/Analysis.cpp +++ b/src/Analysis.cpp @@ -958,7 +958,7 @@ bool Analysis::OpenStreamOutputFiles() ifprintf(vcfLoodosepartial,"##contig=\n",referencePanel.finChromosome.c_str()); ifprintf(vcfLoodosepartial,"##INFO=\n"); ifprintf(vcfLoodosepartial,"##FORMAT=\n"); - ifprintf(vcfLoodosepartial,"##FORMAT=\n"); + ifprintf(vcfLoodosepartial,"##FORMAT=\n"); ifprintf(vcfLoodosepartial,"##minimac4_Command=%s\n",MyAllVariables->myOutFormat.CommandLine.c_str()); ifprintf(vcfLoodosepartial,"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT"); diff --git a/src/DosageData.cpp b/src/DosageData.cpp index 67e2966..e9c5989 100644 --- a/src/DosageData.cpp +++ b/src/DosageData.cpp @@ -297,7 +297,7 @@ void DosageData::PrintDiploidLooDosage(float &x, float &y, AlleleType a, AlleleT PrintEmpStringLength+=sprintf(PrintEmpStringPointer+PrintEmpStringLength,"\t"); PrintEmpStringLength+=sprintf(PrintEmpStringPointer+PrintEmpStringLength,"%c|%c",a,b); PrintEmpStringLength+=sprintf(PrintEmpStringPointer+PrintEmpStringLength,":"); - PrintEmpStringLength+=sprintf(PrintEmpStringPointer+PrintEmpStringLength,"%.3f|%.3f",x , y); + PrintEmpStringLength+=sprintf(PrintEmpStringPointer+PrintEmpStringLength,"%.3f,%.3f",x , y); } @@ -342,7 +342,7 @@ void DosageData::PrintDosageForVcfOutputForID(int MarkerIndex) if( tHapFull->MissingSampleUnscaffolded[gwasHapIndex][TypedMarkerIndex] =='1' || tHapFull->MissingSampleUnscaffolded[gwasHapIndex+1][TypedMarkerIndex]=='1') { - PrintEmpStringLength+=sprintf(PrintEmpStringPointer+PrintEmpStringLength,"\t.|.:.|."); + PrintEmpStringLength+=sprintf(PrintEmpStringPointer+PrintEmpStringLength,"\t.|.:.,."); } else {