Instead of erroring, creating missing indexes

bbimber · bbimber · commit 1c55102fb998 · 2023-06-01T16:18:30.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/GenotypeGVCFsWrapper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/GenotypeGVCFsWrapper.java
@@ -167,7 +167,8 @@ public static List<File> copyVcfsLocally(SequenceOutputHandler.JobContext ctx, C
                     origIdx = new File(f.getPath() + ".tbi");
                     if (!origIdx.exists())
                     {
-                        throw new PipelineJobException("expected index doesn't exist: " + origIdx.getPath());
+                        ctx.getLogger().warn("Expected index does not exist, creating: " + origIdx.getPath());
+                        SequenceAnalysisService.get().ensureVcfIndex(f, ctx.getLogger());
                     }
 
                     movedIdx = new File(localWorkDir, destFile.getName() + ".tbi");

Original file line number	Diff line number	Diff line change
`@@ -167,7 +167,8 @@ public static List<File> copyVcfsLocally(SequenceOutputHandler.JobContext ctx, C`
`167`	`167`	`origIdx = new File(f.getPath() + ".tbi");`
`168`	`168`	`if (!origIdx.exists())`
`169`	`169`	`{`
`170`		`- throw new PipelineJobException("expected index doesn't exist: " + origIdx.getPath());`
	`170`	`+ ctx.getLogger().warn("Expected index does not exist, creating: " + origIdx.getPath());`
	`171`	`+ SequenceAnalysisService.get().ensureVcfIndex(f, ctx.getLogger());`
`171`	`172`	`}`
`172`	`173`
`173`	`174`	`movedIdx = new File(localWorkDir, destFile.getName() + ".tbi");`