Bugfix to lofreq VCF merge

bbimber · bbimber · commit ea56b77aff5f · 2020-07-21T12:55:37.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/MergeLoFreqVcfHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/MergeLoFreqVcfHandler.java
@@ -256,6 +256,11 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
                         //NOTE: deletions spanning this site can also be included, with a start position ahead of this.
                         try (CloseableIterator<VariantContext> it = reader.query(site.getLeft(), site.getRight(), site.getRight()))
                         {
+                            if (!it.hasNext())
+                            {
+                                continue;
+                            }
+
                             VariantContext vc = it.next();
                             if (vc.getAttribute("AF") == null)
                             {

Original file line number	Diff line number	Diff line change
`@@ -256,6 +256,11 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c`
`256`	`256`	`//NOTE: deletions spanning this site can also be included, with a start position ahead of this.`
`257`	`257`	`try (CloseableIterator<VariantContext> it = reader.query(site.getLeft(), site.getRight(), site.getRight()))`
`258`	`258`	`{`
	`259`	`+ if (!it.hasNext())`
	`260`	`+ {`
	`261`	`+ continue;`
	`262`	`+ }`
	`263`	`+`
`259`	`264`	`VariantContext vc = it.next();`
`260`	`265`	`if (vc.getAttribute("AF") == null)`
`261`	`266`	`{`