Add detail to Plink/KING output

bbimber · bbimber · commit 7be1c3acbb2a · 2025-02-11T10:10:55.000-08:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/PlinkPcaStep.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/PlinkPcaStep.java
@@ -231,8 +231,8 @@ private void runBatch(File inputVCF, File outputDirectory, VariantProcessingStep
         String description = null;
         if (kingCutoff != null)
         {
-            long includedIds = SequencePipelineService.get().getLineCount(new File(outputFile.getParentFile(), "plink.king.cutoff.in.id")) - 1;
-            long excludedIds = SequencePipelineService.get().getLineCount(new File(outputFile.getParentFile(), "plink.king.cutoff.out.id")) - 1;
+            long includedIds = SequencePipelineService.get().getLineCount(new File(outputFile.getParentFile(), "plink.king.cutoff.in.id"));
+            long excludedIds = SequencePipelineService.get().getLineCount(new File(outputFile.getParentFile(), "plink.king.cutoff.out.id"));
 
             description = String.format("KING cutoff: %f, included IDs: %d, excluded IDs: %d", kingCutoff, includedIds, excludedIds);
         }

Original file line number	Diff line number	Diff line change
`@@ -231,8 +231,8 @@ private void runBatch(File inputVCF, File outputDirectory, VariantProcessingStep`
`231`	`231`	`String description = null;`
`232`	`232`	`if (kingCutoff != null)`
`233`	`233`	`{`
`234`		`- long includedIds = SequencePipelineService.get().getLineCount(new File(outputFile.getParentFile(), "plink.king.cutoff.in.id")) - 1;`
`235`		`- long excludedIds = SequencePipelineService.get().getLineCount(new File(outputFile.getParentFile(), "plink.king.cutoff.out.id")) - 1;`
	`234`	`+ long includedIds = SequencePipelineService.get().getLineCount(new File(outputFile.getParentFile(), "plink.king.cutoff.in.id"));`
	`235`	`+ long excludedIds = SequencePipelineService.get().getLineCount(new File(outputFile.getParentFile(), "plink.king.cutoff.out.id"));`
`236`	`236`
`237`	`237`	`description = String.format("KING cutoff: %f, included IDs: %d, excluded IDs: %d", kingCutoff, includedIds, excludedIds);`
`238`	`238`	`}`