Bugfix to merge lofreq VCFs

bbimber · bbimber · commit e44e027f5854 · 2020-07-21T06:54:59.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/MergeLoFreqVcfHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/MergeLoFreqVcfHandler.java
@@ -111,7 +111,7 @@ private class SiteAndAlleles
             private final Allele _ref;
 
             Map<String, Map<Allele, Allele>> _encounteredAlleles = new HashMap<>();
-            List<Allele> _alternates;
+            List<Allele> _alternates = new ArrayList<>();
 
             public SiteAndAlleles(String contig, int start, Allele ref)
             {

Original file line number	Diff line number	Diff line change
`@@ -111,7 +111,7 @@ private class SiteAndAlleles`
`111`	`111`	`private final Allele _ref;`
`112`	`112`
`113`	`113`	`Map<String, Map<Allele, Allele>> _encounteredAlleles = new HashMap<>();`
`114`		`- List<Allele> _alternates;`
	`114`	`+ List<Allele> _alternates = new ArrayList<>();`
`115`	`115`
`116`	`116`	`public SiteAndAlleles(String contig, int start, Allele ref)`
`117`	`117`	`{`