Adjust location of VCF index tasks to better allow resume

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ProcessVariantsHandler.java

@@ -369,15 +369,6 @@ public static List<Interval> getIntervals(JobContext ctx)
 
     public static File processVCF(File input, Integer libraryId, JobContext ctx, Resumer resumer, boolean subsetToIntervals) throws PipelineJobException
     {
-        try
-        {
-            SequenceAnalysisService.get().ensureVcfIndex(input, ctx.getLogger());
-        }
-        catch (IOException e)
-        {
-            throw new PipelineJobException(e);
-        }
-
         File currentVCF = input;
 
         ctx.getJob().getLogger().info("***Starting processing of file: " + input.getName());
@@ -409,6 +400,15 @@ public static File processVCF(File input, Integer libraryId, JobContext ctx, Res
             }
             else
             {
+                try
+                {
+                    SequenceAnalysisService.get().ensureVcfIndex(input, ctx.getLogger());
+                }
+                catch (IOException e)
+                {
+                    throw new PipelineJobException(e);
+                }
+
                 OutputVariantsStartingInIntervalsStep.Wrapper wrapper = new OutputVariantsStartingInIntervalsStep.Wrapper(ctx.getLogger());
                 wrapper.execute(input, outputFile, getIntervals(ctx));
             }
@@ -432,6 +432,15 @@ public static File processVCF(File input, Integer libraryId, JobContext ctx, Res
                 continue;
             }
 
+            try
+            {
+                SequenceAnalysisService.get().ensureVcfIndex(input, ctx.getLogger());
+            }
+            catch (IOException e)
+            {
+                throw new PipelineJobException(e);
+            }
+
             RecordedAction action = new RecordedAction(stepCtx.getProvider().getLabel());
             Date start = new Date();
             action.setStartTime(start);