Bugfix to CellRangerVDJWrapper

Author: bbimber

singlecell/api-src/org/labkey/api/singlecell/CellHashingService.java

@@ -127,7 +127,7 @@ public static CellHashingService.CellHashingParameters createFromStep(SequenceOu
             ret.majorityConsensusThreshold = step.getProvider().getParameterByName("majorityConsensusThreshold").extractValue(ctx.getJob(), step.getProvider(), step.getStepIdx(), Double.class, null);
             ret.minAllowableDoubletRateFilter = step.getProvider().getParameterByName("minAllowableDoubletRateFilter").extractValue(ctx.getJob(), step.getProvider(), step.getStepIdx(), Double.class, null);
             ret.callerDisagreementThreshold = step.getProvider().getParameterByName("callerDisagreementThreshold").extractValue(ctx.getJob(), step.getProvider(), step.getStepIdx(), Double.class, null);
-            ret.doTSNE = step.getProvider().getParameterByName("doTSNE").extractValue(ctx.getJob(), step.getProvider(), step.getStepIdx(), Boolean.class, null);
+            ret.doTSNE = step.getProvider().getParameterByName("doTSNE").extractValue(ctx.getJob(), step.getProvider(), step.getStepIdx(), Boolean.class, false);
             ret.retainRawCountFile = step.getProvider().getParameterByName("retainRawCountFile").extractValue(ctx.getJob(), step.getProvider(), step.getStepIdx(), Boolean.class, true);
             ret.failIfUnexpectedHtosFound = step.getProvider().getParameterByName("failIfUnexpectedHtosFound").extractValue(ctx.getJob(), step.getProvider(), step.getStepIdx(), Boolean.class, true);
             ret.htoReadset = htoReadset;
@@ -170,7 +170,7 @@ public static CellHashingParameters createFromJson(BARCODE_TYPE type, File webse
             ret.majorityConsensusThreshold = params.get("majorityConsensusThreshold") == null ? null : params.getDouble("majorityConsensusThreshold");
             ret.minAllowableDoubletRateFilter = params.get("minAllowableDoubletRateFilter") == null ? null : params.getDouble("minAllowableDoubletRateFilter");
             ret.callerDisagreementThreshold = params.get("callerDisagreementThreshold") == null ? null : params.getDouble("callerDisagreementThreshold");
-            ret.doTSNE = params.get("doTSNE") == null || params.getBoolean("doTSNE");
+            ret.doTSNE = params.get("doTSNE") == null || params.optBoolean("doTSNE", false);
             ret.retainRawCountFile = params.optBoolean("retainRawCountFile", true);
             ret.failIfUnexpectedHtosFound = params.optBoolean("failIfUnexpectedHtosFound", true);
             ret.htoReadset = htoReadset;

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

@@ -473,7 +473,13 @@ private File processOutputsForType(String sampleId, Readset rs, ReferenceGenome
             {
                 try
                 {
-                    FileUtils.moveFile(f, new File(sampleDir, f.getName()));
+                    File dest = new File(sampleDir, f.getName());
+                    if (dest.exists())
+                    {
+                        dest.delete();
+                    }
+
+                    FileUtils.moveFile(f, dest);
                 }
                 catch (IOException e)
                 {
@@ -911,22 +917,22 @@ else if (idx == 9)
                         uniqueChains.clear();
                         uniqueChains.add(cGeneChain);
                         String key = originalChain + "->" + cGeneChain + " (based on C-GENE)";
-                        chimericCallsRecovered.put(key, chimericCallsRecovered.getOrDefault(key, 0));
+                        chimericCallsRecovered.put(key, chimericCallsRecovered.getOrDefault(key, 0) + 1);
                     }
                     else if (uniqueChains.size() == 2)
                     {
                         if ("TRD".equals(vGeneChain) && "TRA".equals(jGeneChain))
                         {
                             uniqueChains.clear();
                             String key = originalChain + "->" + vGeneChain + " (based on V-GENE)";
-                            chimericCallsRecovered.put(key, chimericCallsRecovered.getOrDefault(key, 0));
+                            chimericCallsRecovered.put(key, chimericCallsRecovered.getOrDefault(key, 0) + 1);
                             uniqueChains.add(vGeneChain);
                         }
                         if ("TRA".equals(vGeneChain) && "TRD".equals(jGeneChain))
                         {
                             uniqueChains.clear();
                             String key = originalChain + "->" + vGeneChain + " (based on V-GENE)";
-                            chimericCallsRecovered.put(key, chimericCallsRecovered.getOrDefault(key, 0));
+                            chimericCallsRecovered.put(key, chimericCallsRecovered.getOrDefault(key, 0) + 1);
                             uniqueChains.add(vGeneChain);
                         }
                     }