More permissive locus splitting in cellranger vdj library prep

bbimber · bbimber · commit f3a20a016aa3 · 2021-06-23T04:37:15.000-07:00
diff --git a/singlecell/src/org/labkey/singlecell/run/CellRangerVDJWrapper.java b/singlecell/src/org/labkey/singlecell/run/CellRangerVDJWrapper.java
@@ -148,7 +148,7 @@ public void init(SequenceAnalysisJobSupport support) throws PipelineJobException
                         }
 
                         //NOTE: this allows dual TRA/TRD segments
-                        String[] loci = nt.getLocus().split("/");
+                        String[] loci = nt.getLocus().split("[/,]");
                         for (String locus : loci)
                         {
                             i.getAndIncrement(); //cant use sequenceId since sequences might be represented multiple times across loci

Original file line number	Diff line number	Diff line change
`@@ -148,7 +148,7 @@ public void init(SequenceAnalysisJobSupport support) throws PipelineJobException`
`148`	`148`	`}`
`149`	`149`
`150`	`150`	`//NOTE: this allows dual TRA/TRD segments`
`151`		`- String[] loci = nt.getLocus().split("/");`
	`151`	`+ String[] loci = nt.getLocus().split("[/,]");`
`152`	`152`	`for (String locus : loci)`
`153`	`153`	`{`
`154`	`154`	`i.getAndIncrement(); //cant use sequenceId since sequences might be represented multiple times across loci`