Switch approach for differentiating TRD/G segments in cellranger

Author: bbimber

cluster/src/org/labkey/cluster/pipeline/AbstractClusterExecutionEngine.java

@@ -502,9 +502,9 @@ protected void updateJobStatus(@Nullable String status, ClusterJob j, @Nullable
                 statusChanged = true;
             }
 
-            if (!statusChanged && !sf.getStatus().equalsIgnoreCase(j.getStatus()))
+            if (status != null && !statusChanged && !sf.getStatus().equalsIgnoreCase(j.getStatus()))
             {
-                _log.error("ClusterExecutionEngine reports status not changed, but was: " + status + " / statusfile: " + sf.getStatus() + " / cluster job: " + j.getStatus());
+                _log.error("ClusterExecutionEngine reports status not changed for job: " + sf.getRowId() + ", but was: " + status + " / statusfile: " + sf.getStatus() + " / cluster job: " + j.getStatus());
             }
         }
 

singlecell/src/org/labkey/singlecell/run/CellRangerVDJWrapper.java

@@ -167,20 +167,23 @@ public void init(SequenceAnalysisJobSupport support) throws PipelineJobException
 
                             //example: >1|TRAV41*01 TRAV41|TRAV41|L-REGION+V-REGION|TR|TRA|None|None
                             //Note: for g/d recovery, add any gamma segments as TRA and delta as TRB. Also prefix their gene names with TRA/B, but keep the true name (i.e. TRDV1 -> TRBTRDV1)
-                            String prefix = "";
+                            String suffix = "";
+                            String lineage = nt.getLineage();
                             if (doGDParsing() && "TRD".equalsIgnoreCase(locus))
                             {
-                                prefix = "TRB";
+                                suffix = "d";
+                                lineage = lineage.replaceAll("TRD", "TRB");
                                 locus = "TRB";
                             }
                             else if (doGDParsing() && "TRG".equalsIgnoreCase(locus))
                             {
-                                prefix = "TRA";
+                                suffix = "g";
+                                lineage = lineage.replaceAll("TRG", "TRA");
                                 locus = "TRA";
                             }
 
                             StringBuilder header = new StringBuilder();
-                            header.append(">").append(i.get()).append("|").append(prefix).append(nt.getName()).append(" ").append(prefix).append(nt.getLineage()).append("|").append(prefix).append(nt.getLineage()).append("|");
+                            header.append(">").append(i.get()).append("|").append(nt.getName()).append(suffix).append(" ").append(lineage).append("|").append(lineage).append("|");
                             //translate into V_Region
                             String type;
                             if (nt.getLineage().contains("J"))
@@ -235,7 +238,7 @@ private File getGenomeFasta()
         @Override
         public String getIndexCachedDirName(PipelineJob job)
         {
-            return getProvider().getName() + (doGDParsing() ? "-GD" : "");
+            return getProvider().getName() + (doGDParsing() ? "-GammaDelta" : "");
         }
 
         @Override
@@ -431,7 +434,7 @@ public AlignmentStep.AlignmentOutput performAlignment(Readset rs, List<File> inp
                         int totalG = 0;
                         while ((line = reader.readLine()) != null)
                         {
-                            if (line.contains("TRATRG") || line.contains("TRBTRD"))
+                            if (line.contains("g,") || line.contains("d,"))
                             {
                                 //Infer correct chain from the V, J and C genes
                                 String[] tokens = line.split(",");
@@ -443,11 +446,11 @@ public AlignmentStep.AlignmentOutput performAlignment(Readset rs, List<File> inp
                                     String val = StringUtils.trimToNull(tokens[idx]);
                                     if (val != null)
                                     {
-                                        if (val.contains("TRATRG"))
+                                        if (val.endsWith("g"))
                                         {
                                             val = "TRG";
                                         }
-                                        else if (val.contains("TRBTRD"))
+                                        else if (val.endsWith("d"))
                                         {
                                             val = "TRD";
                                         }
@@ -523,8 +526,8 @@ else if (chain.equals("TRD"))
                                     tokens[5] = chain;
 
                                     line = StringUtils.join(tokens, ",");
-                                    line = line.replaceAll("TRATRG", "TRG");
-                                    line = line.replaceAll("TRBTRD", "TRD");
+                                    line = line.replaceAll("g,", ",");
+                                    line = line.replaceAll("d,", ",");
                                 }
                                 else
                                 {