- Expand SDA plotting

- Allow TCR cell hashing to use demuxEM

Author: bbimber

tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJCellHashingHandler.java

@@ -62,12 +62,9 @@ private static List<ToolParameterDescriptor> getDefaultParams()
                 ToolParameterDescriptor.create("useOutputFileContainer", "Submit to Source File Workbook", "If checked, each job will be submitted to the same workbook as the input file, as opposed to submitting all jobs to the same workbook.  This is primarily useful if submitting a large batch of files to process separately. This only applies if 'Run Separately' is selected.", "checkbox", new JSONObject(){{
                     put("checked", true);
                 }}, false)
-//                ToolParameterDescriptor.create(USE_GEX_BARCODES, "Use GEX and TCR Cell Barcodes", "If checked, the cell barcode whitelist used for cell hashing will be the union of TCR and GEX cell barcodes. If T-cells are a rare component of total cells, this might enhance the effectiveness of the callers by providing more positive signal.", "checkbox", new JSONObject(){{
-//                    put("checked", true);
-//                }}, false)
         ));
 
-        ret.addAll(CellHashingService.get().getHashingCallingParams(false));
+        ret.addAll(CellHashingService.get().getHashingCallingParams(true));
 
         return ret;
     }
@@ -114,14 +111,7 @@ public class Processor implements SequenceOutputHandler.SequenceOutputProcessor
         public void init(JobContext ctx, List<SequenceOutputFile> inputFiles, List<RecordedAction> actions, List<SequenceOutputFile> outputsToCreate) throws UnsupportedOperationException, PipelineJobException
         {
             //NOTE: this is the pathway to import assay data, whether hashing is used or not
-            CellHashingService.get().prepareHashingForVdjIfNeeded(ctx.getOutputDir(), ctx.getJob(), ctx.getSequenceSupport(), "tcrReadsetId", false);
-
-            if (ctx.getParams().optBoolean(USE_GEX_BARCODES, false))
-            {
-                ctx.getJob().getLogger().info("The union of TCR and GEX cell barcodes will be used for calling");
-                Map<Integer, File> vLoupeIdToGexBarcodeDir = new HashMap<>();
-
-            }
+            CellHashingService.get().prepareHashingForVdjIfNeeded(ctx, false);
         }
 
         @Override