Make ConvertToCramHandler more tolerant to job restarts

Author: bbimber

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/SamtoolsCramConverter.java

@@ -72,10 +72,15 @@ private void doIndex(File input, @Nullable Integer threads) throws PipelineJobEx
         params.add(input.getPath());
         execute(params);
 
-        File idx = new File(input.getPath() + ".crai");
+        File idx = getExpectedCramIndex(input);
         if (!idx.exists())
         {
             throw new PipelineJobException("Unable to find CRAM index: " + idx.getPath());
         }
     }
+
+    public static File getExpectedCramIndex(File input)
+    {
+        return new File(input.getPath() + ".crai");
+    }
 }

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

@@ -109,14 +109,37 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
             {
                 ReferenceGenome genome = ctx.getSequenceSupport().getCachedGenome(so.getLibrary_id());
                 File cram = new File(so.getFile().getParentFile(), FileUtil.getBaseName(so.getFile()) + ".cram");
-                new SamtoolsCramConverter(ctx.getLogger()).convert(so.getFile(), cram, genome.getWorkingFastaFileGzipped(), true, threads);
+                File cramIdx = SamtoolsCramConverter.getExpectedCramIndex(cram);
+                if (!so.getFile().exists())
+                {
+                    if (replaceOriginal && cramIdx.exists())
+                    {
+                        ctx.getLogger().debug("BAM does not exist, but CRAM index does. Proceeding on the assumption this is a resume of a failed job.");
+                    }
+                    else
+                    {
+                        throw new PipelineJobException("Unable to find BAM: " + so.getFile().getPath());
+                    }
+                }
+                else
+                {
+                    new SamtoolsCramConverter(ctx.getLogger()).convert(so.getFile(), cram, genome.getWorkingFastaFileGzipped(), true, threads);
+                }
+
                 checkCramAndIndex(so);
 
                 if (replaceOriginal)
                 {
                     ctx.getLogger().info("Deleting original BAM: " + so.getFile().getPath());
-                    new File(so.getFile().getPath() + ".bai").delete();
-                    so.getFile().delete();
+                    if (so.getFile().exists())
+                    {
+                        new File(so.getFile().getPath() + ".bai").delete();
+                        so.getFile().delete();
+                    }
+                    else
+                    {
+                        ctx.getLogger().debug("Input BAM not found, possibly deleted in earlier job iteration?");
+                    }
                 }
             }
         }