Allow nextclade AA import to skip complex indels

bbimber · bbimber · commit 812f2580d33a · 2021-10-30T17:22:39.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/NextCladeHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/NextCladeHandler.java
@@ -345,6 +345,12 @@ public static void processAndImportNextCladeAa(PipelineJob job, File jsonFile, i
             if (vcList.isEmpty())
             {
                 job.getLogger().error("Cannot find matching NT SNP: " + aa.toString());
+                if (aa.containsKey("refContext") && aa.getString("refContext").length() > 4)
+                {
+                    // Skip complex indels with just a logged error, but let the job finish
+                    continue;
+                }
+
                 throw new PipelineJobException("Expected variant for AA position: " + aaName + " " + pos);
             }
 

Original file line number	Diff line number	Diff line change
`@@ -345,6 +345,12 @@ public static void processAndImportNextCladeAa(PipelineJob job, File jsonFile, i`
`345`	`345`	`if (vcList.isEmpty())`
`346`	`346`	`{`
`347`	`347`	`job.getLogger().error("Cannot find matching NT SNP: " + aa.toString());`
	`348`	`+ if (aa.containsKey("refContext") && aa.getString("refContext").length() > 4)`
	`349`	`+ {`
	`350`	`+ // Skip complex indels with just a logged error, but let the job finish`
	`351`	`+ continue;`
	`352`	`+ }`
	`353`	`+`
`348`	`354`	`throw new PipelineJobException("Expected variant for AA position: " + aaName + " " + pos);`
`349`	`355`	`}`
`350`	`356`