From f83e55ab5dc704da586d56826424070f15bca493 Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Mon, 24 Feb 2025 06:47:31 -0800
Subject: [PATCH] Bugfix to KING resume

---
 .../run/variant/KingInferenceStep.java        | 51 ++++++++++---------
 1 file changed, 26 insertions(+), 25 deletions(-)

diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/KingInferenceStep.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/KingInferenceStep.java
index a1b3b9af5..9a21691b5 100644
--- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/KingInferenceStep.java
+++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/KingInferenceStep.java
@@ -172,47 +172,48 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno
         plinkArgs2.add(plinkOutKing.getPath());
 
         doneFile = new File (plinkOutKing.getPath() + ".done");
+        File plinkOutKingFile = new File(plinkOutKing.getPath() + ".kin0");
+        File plinkOutKingFileGz = new File(plinkOutKingFile.getPath() + ".txt.gz");
         if (doneFile.exists())
         {
             getPipelineCtx().getLogger().debug("plink has completed, will not repeat");
         }
-        else {
+        else
+        {
             plink.execute(plinkArgs2);
 
+            if (!plinkOutKingFile.exists())
+            {
+                throw new PipelineJobException("Unable to find file: " + plinkOutKingFile.getPath());
+            }
+
+            if (plinkOutKingFileGz.exists())
+            {
+                plinkOutKingFileGz.delete();
+            }
+
             try
             {
-                Files.touch(doneFile);
+                Compress.compressGzip(plinkOutKingFile, plinkOutKingFileGz);
+                FileUtils.delete(plinkOutKingFile);
             }
             catch (IOException e)
             {
                 throw new PipelineJobException(e);
             }
-        }
-
-        File plinkOutKingFile = new File(plinkOutKing.getPath() + ".kin0");
-        if (!plinkOutKingFile.exists())
-        {
-            throw new PipelineJobException("Unable to find file: " + plinkOutKingFile.getPath());
-        }
 
-        File plinkOutKingFileTxt = new File(plinkOutKingFile.getPath() + ".txt.gz");
-        if (plinkOutKingFileTxt.exists())
-        {
-            plinkOutKingFileTxt.delete();
-        }
-
-        long lineCount = SequencePipelineService.get().getLineCount(plinkOutKingFile)-1;
-        try
-        {
-            Compress.compressGzip(plinkOutKingFile, plinkOutKingFileTxt);
-            FileUtils.delete(plinkOutKingFile);
-        }
-        catch (IOException e)
-        {
-            throw new PipelineJobException(e);
+            try
+            {
+                Files.touch(doneFile);
+            }
+            catch (IOException e)
+            {
+                throw new PipelineJobException(e);
+            }
         }
 
-        output.addSequenceOutput(plinkOutKingFileTxt, "PLINK2/KING Relatedness: " + inputVCF.getName(), "PLINK2/KING Kinship", null, null, genome.getGenomeId(), "Total lines: " + lineCount);
+        long lineCount = SequencePipelineService.get().getLineCount(plinkOutKingFileGz)-1;
+        output.addSequenceOutput(plinkOutKingFileGz, "PLINK2/KING Relatedness: " + inputVCF.getName(), "PLINK2/KING Kinship", null, null, genome.getGenomeId(), "Total lines: " + lineCount);
 
         return output;
     }