Bugfix LoFreq variant import

bbimber · bbimber · commit 1cef6be26380 · 2021-03-15T16:48:34.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/NextCladeHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/NextCladeHandler.java
@@ -267,7 +267,8 @@ public static void processAndImportNextCladeAa(PipelineJob job, File jsonFile, i
 
             JSONObject range = aa.getJSONObject("nucRange");
             List<Integer> positions = new ArrayList<>();
-            for (int p = range.getInt("begin");p <= range.getInt("end"); p++)
+            //Range is 0-based
+            for (int p = range.getInt("begin") + 1;p <= range.getInt("end"); p++)
             {
                 positions.add(p);
             }

Original file line number	Diff line number	Diff line change
`@@ -267,7 +267,8 @@ public static void processAndImportNextCladeAa(PipelineJob job, File jsonFile, i`
`267`	`267`
`268`	`268`	`JSONObject range = aa.getJSONObject("nucRange");`
`269`	`269`	`List<Integer> positions = new ArrayList<>();`
`270`		`- for (int p = range.getInt("begin");p <= range.getInt("end"); p++)`
	`270`	`+ //Range is 0-based`
	`271`	`+ for (int p = range.getInt("begin") + 1;p <= range.getInt("end"); p++)`
`271`	`272`	`{`
`272`	`273`	`positions.add(p);`
`273`	`274`	`}`