Update gVCF index locator in GLNexus step

bbimber · bbimber · commit 45d7f145779f · 2024-01-31T09:37:29.000-08:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GLNexusHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GLNexusHandler.java
@@ -212,7 +212,7 @@ public void execute(List<File> inputGvcfs, File outputVcf, PipelineOutputTracker
             for (File f : inputGvcfs)
             {
                 gvcfsLocal.add(ensureLocalCopy(f, workDir, tracker));
-                ensureLocalCopy(SequenceUtil.getExpectedIndex(f), workDir, tracker);
+                ensureLocalCopy(new File(f.getPath() + ".tbi"), workDir, tracker);
             }
 
             File localBashScript = new File(workDir, "docker.sh");

Original file line number	Diff line number	Diff line change
`@@ -212,7 +212,7 @@ public void execute(List<File> inputGvcfs, File outputVcf, PipelineOutputTracker`
`212`	`212`	`for (File f : inputGvcfs)`
`213`	`213`	`{`
`214`	`214`	`gvcfsLocal.add(ensureLocalCopy(f, workDir, tracker));`
`215`		`- ensureLocalCopy(SequenceUtil.getExpectedIndex(f), workDir, tracker);`
	`215`	`+ ensureLocalCopy(new File(f.getPath() + ".tbi"), workDir, tracker);`
`216`	`216`	`}`
`217`	`217`
`218`	`218`	`File localBashScript = new File(workDir, "docker.sh");`