Remove noise from orphan file job and protect from exceptions in maintenance task

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisMaintenanceTask.java

@@ -341,6 +341,7 @@ private void processContainer(Container c, Logger log) throws IOException
                     if (!d.getFile().exists())
                     {
                         log.error("expected output file does not exist: " + d.getFile().getPath());
+                        continue;
                     }
 
                     //also verify indexes

SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/OrphanFilePipelineJob.java

@@ -554,6 +554,19 @@ else if (f.getPath().contains("/Normalization/") && f.getName().contains("_unkno
                                     continue;
                                 else if (f.getPath().contains("/outs/") || f.getPath().contains("/Alignment/") && (f.getName().contains("unaligned") || f.getName().contains("unmapped") || f.getName().contains(".overlapping-")))
                                     continue;
+                                else if (f.getName().contains(".overlapping-R"))
+                                {
+                                    //outputs from earlier TCR pipelines:
+                                    continue;
+                                }
+                            }
+                            else if (SequenceUtil.FILETYPE.bam.getFileType().isType(f))
+                            {
+                                //ignore 10x products:
+                                if (f.getPath().contains("/outs/"))
+                                {
+                                    continue;
+                                }
                             }
 
                             //this is too broad a net

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/MergeLoFreqVcfHandler.java

@@ -500,7 +500,7 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
                                     double diff = Math.abs(adjAF - af);
                                     if (diff > 0.01)
                                     {
-                                        ctx.getLogger().warn("Significant AF adjustment: readset: " + line.get(0) + " / site: " + line.get(4) + " / allele: " + a + " / AF: " + af + " / New AF" + adjAF + " / diff: " + diff + " / gatk depth: " + gatkDepth + " / lofreq depth: " + lofreqDepth);
+                                        ctx.getLogger().warn("Significant AF adjustment: readset: " + line.get(0) + " / site: " + line.get(4) + " / allele: " + a + " / AF: " + af + " / New AF: " + adjAF + " / diff: " + diff + " / gatk depth: " + gatkDepth + " / lofreq depth: " + lofreqDepth);
                                     }
 
                                     totalAltAf += adjAF;