Bugfix for lofreq vcf merge

bbimber · bbimber · commit 714f1a5d1ee0 · 2020-07-16T12:07:56.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/MergeLoFreqVcfHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/MergeLoFreqVcfHandler.java
@@ -320,7 +320,7 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
                                     line.add("");
                                     line.add(String.valueOf(depth));
                                     line.add("1");
-                                    line.add(";0".repeat(siteDef._alternates.size() - 1).substring(1));
+                                    line.add(";0".repeat(siteDef._alternates.size()).substring(1));
                                 }
 
                                 writer.writeNext(line.toArray(new String[]{}));

Original file line number	Diff line number	Diff line change
`@@ -320,7 +320,7 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c`
`320`	`320`	`line.add("");`
`321`	`321`	`line.add(String.valueOf(depth));`
`322`	`322`	`line.add("1");`
`323`		`- line.add(";0".repeat(siteDef._alternates.size() - 1).substring(1));`
	`323`	`+ line.add(";0".repeat(siteDef._alternates.size()).substring(1));`
`324`	`324`	`}`
`325`	`325`
`326`	`326`	`writer.writeNext(line.toArray(new String[]{}));`