Preserve empty cells when parsing all_contigs CSV from cellranger vdj

Author: bbimber

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

@@ -516,7 +516,7 @@ protected void updateJobStatus(@Nullable String status, ClusterJob j, @Nullable
         // Because it is possible for a prior submission to report a status, only update the PipelineJob itself if this is the latest submission.
         if (hasNewerSubmission)
         {
-            //_log.info("There is a newer submission for job: " + sf.getRowId() + ". Skipping update for cluster ID: " + j.getClusterId() + " in favor of " + mostRecent.getClusterId());
+            //_log.info("There is a newer submission for job: " + (sf == null ? null : sf.getRowId()) + ". Skipping update for cluster ID: " + j.getClusterId() + " in favor of " + mostRecent.getClusterId());
             statusChanged = false;
         }
 

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

@@ -478,7 +478,7 @@ public AlignmentStep.AlignmentOutput performAlignment(Readset rs, List<File> inp
                             if (lineIdx > 1 && (line.contains("g,") || line.contains("d,")))
                             {
                                 //Infer correct chain from the V, J and C genes
-                                String[] tokens = line.split(",");
+                                String[] tokens = line.split(",", -1);  // -1 used to preserve trailing empty strings
                                 List<String> chains = new ArrayList<>();
                                 String vGeneChain = null;
                                 String jGeneChain = null;