Change LDS format from string to number, change delimiter for LDS fro…

…m vertical slash to comma
statgen · Aug 17, 2021 · 8498da5 · 8498da5
1 parent ebbe6bd
commit 8498da5
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/src/Analysis.cpp b/src/Analysis.cpp
@@ -958,7 +958,7 @@ bool Analysis::OpenStreamOutputFiles()
         ifprintf(vcfLoodosepartial,"##contig=<ID=%s>\n",referencePanel.finChromosome.c_str());
         ifprintf(vcfLoodosepartial,"##INFO=<ID=TYPED,Number=0,Type=Flag,Description=\"Marker was genotyped AND imputed\">\n");
         ifprintf(vcfLoodosepartial,"##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotyped alleles from Array\">\n");
-        ifprintf(vcfLoodosepartial,"##FORMAT=<ID=LDS,Number=1,Type=String,Description=\"Leave-one-out Imputed Dosage : Estimated Haploid Alternate Allele Dosage assuming site was NOT genotyped \">\n");
+        ifprintf(vcfLoodosepartial,"##FORMAT=<ID=LDS,Number=2,Type=Float,Description=\"Leave-one-out Imputed Dosage : Estimated Haploid Alternate Allele Dosage assuming site was NOT genotyped \">\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
@@ -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
                  {