Bugfix LoFreq variant import

bbimber · bbimber · commit 97c9158aeb04 · 2021-03-15T19:42:31.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/NextCladeHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/NextCladeHandler.java
@@ -269,6 +269,8 @@ public static void processAndImportNextCladeAa(PipelineJob job, File jsonFile, i
         {
             JSONObject aa = aaSubstitutions.getJSONObject(i);
             int pos = aa.getInt("codon");
+            pos = pos + 1; //make 1-based
+
             String aaName = aa.getString("gene");
 
             JSONObject range = aa.getJSONObject("nucRange");

Original file line number	Diff line number	Diff line change
`@@ -269,6 +269,8 @@ public static void processAndImportNextCladeAa(PipelineJob job, File jsonFile, i`
`269`	`269`	`{`
`270`	`270`	`JSONObject aa = aaSubstitutions.getJSONObject(i);`
`271`	`271`	`int pos = aa.getInt("codon");`
	`272`	`+ pos = pos + 1; //make 1-based`
	`273`	`+`
`272`	`274`	`String aaName = aa.getString("gene");`
`273`	`275`
`274`	`276`	`JSONObject range = aa.getJSONObject("nucRange");`