Bugfix to mGAPReleaseGenerator and VCF indexes

bbimber · bbimber · commit 0969e2b2d61a · 2023-12-05T06:09:36.000-08:00
diff --git a/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java b/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java
@@ -432,10 +432,10 @@ else if (so.getCategory().endsWith("Release Track"))
                     throw new PipelineJobException("Unable to find novel sites VCF for release: " + release);
                 }
 
-                SequenceOutputFile luceneIndex = JBrowseService.get().findMatchingLuceneIndex(inputs.get(0), IndexVariantsForMgapStep.getInfoFieldsToIndex(job.getContainer(), job.getUser()), job.getUser(), job.getLogger());
+                SequenceOutputFile luceneIndex = JBrowseService.get().findMatchingLuceneIndex(so, IndexVariantsForMgapStep.getInfoFieldsToIndex(job.getContainer(), job.getUser()), job.getUser(), job.getLogger());
                 if (luceneIndex == null)
                 {
-                    throw new PipelineJobException("Unable to lucene index matching the input VCF: " + inputs.get(0).getFile().getPath());
+                    throw new PipelineJobException("Unable to lucene index matching the input VCF: " + so.getFile().getPath());
                 }
 
                 //find basic stats:

Original file line number	Diff line number	Diff line change
`@@ -432,10 +432,10 @@ else if (so.getCategory().endsWith("Release Track"))`
`432`	`432`	`throw new PipelineJobException("Unable to find novel sites VCF for release: " + release);`
`433`	`433`	`}`
`434`	`434`
`435`		`- SequenceOutputFile luceneIndex = JBrowseService.get().findMatchingLuceneIndex(inputs.get(0), IndexVariantsForMgapStep.getInfoFieldsToIndex(job.getContainer(), job.getUser()), job.getUser(), job.getLogger());`
	`435`	`+ SequenceOutputFile luceneIndex = JBrowseService.get().findMatchingLuceneIndex(so, IndexVariantsForMgapStep.getInfoFieldsToIndex(job.getContainer(), job.getUser()), job.getUser(), job.getLogger());`
`436`	`436`	`if (luceneIndex == null)`
`437`	`437`	`{`
`438`		`- throw new PipelineJobException("Unable to lucene index matching the input VCF: " + inputs.get(0).getFile().getPath());`
	`438`	`+ throw new PipelineJobException("Unable to lucene index matching the input VCF: " + so.getFile().getPath());`
`439`	`439`	`}`
`440`	`440`
`441`	`441`	`//find basic stats:`