Add quicker validation over unknown ADT panels

Author: bbimber

singlecell/src/org/labkey/singlecell/CellHashingServiceImpl.java

@@ -488,6 +488,11 @@ private void writeCiteSeqBarcodes(PipelineJob job, Map<Integer, Set<String>> gex
                     metaWriter.writeNext(new String[]{results.getString(FieldKey.fromString("antibody")), results.getString(FieldKey.fromString("antibody/adaptersequence")), name, label, results.getString(FieldKey.fromString("antibody/barcodePattern"))});
                 });
 
+                if (barcodeCount.get() == 0)
+                {
+                    throw new PipelineJobException("No barcodes found for readset: " + gexReadsetId + " with ADT panel: " + StringUtils.join(gexToPanels.get(gexReadsetId), ", "));
+                }
+
                 job.getLogger().info("Total CITE-seq barcodes written: " + barcodeCount.get());
             }
             catch (IOException e)

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

@@ -379,15 +379,22 @@ private File createFeatureRefForCiteSeq(File outputDir, File adtWhitelist) throw
 
                 //Example: TotalSeq-C-161,CD11b,R2,5PNNNNNNNNNN(BC),GACAAGTGATCTGCA,Antibody Capture
                 String[] line;
+                int total = 0;
                 while ((line = reader.readNext()) != null)
                 {
                     if ("tagname".equals(line[0]))
                     {
                         continue;
                     }
 
+                    total++;
                     writer.writeNext(new String[]{line[0], line[2].replaceAll("_", "-"), "R2", line[4], line[1], "Antibody Capture"});
                 }
+
+                if (total == 0)
+                {
+                    throw new PipelineJobException("There were no ADT features!");
+                }
             }
             catch (IOException e)
             {