Bugfix to sawfish

Author: bbimber

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

@@ -92,15 +92,24 @@ public Output performAnalysisPerSampleRemote(Readset rs, File inputBam, Referenc
             args.add(String.valueOf(maxThreads));
         }
 
-        new SimpleScriptWrapper(getPipelineCtx().getLogger()).execute(args);
+        File bcf = new File(svOutDir, "candidate.sv.bcf");
+        File bcfIdx = new File(bcf.getPath() + ".csi");
+        if (bcfIdx.exists())
+        {
+            getPipelineCtx().getLogger().debug("BCF index already exists, reusing output");
+        }
+        else
+        {
+            new SimpleScriptWrapper(getPipelineCtx().getLogger()).execute(args);
+        }
 
-        File vcf = new File(svOutDir, "genotyped.sv.vcf.gz");
-        if (!vcf.exists())
+        if (!bcf.exists())
         {
-            throw new PipelineJobException("Unable to find file: " + vcf.getPath());
+            throw new PipelineJobException("Unable to find file: " + bcf.getPath());
         }
 
-        output.addSequenceOutput(vcf, rs.getName() + ": sawfish", "Sawfish SV Discovery", rs.getReadsetId(), null, referenceGenome.getGenomeId(), null);
+        output.addSequenceOutput(bcf, rs.getName() + ": sawfish", "Sawfish SV Discovery", rs.getReadsetId(), null, referenceGenome.getGenomeId(), null);
+
         return output;
     }
 

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

@@ -43,7 +43,7 @@ public SawfishJointCallingHandler()
     @Override
     public boolean canProcess(SequenceOutputFile o)
     {
-        return o.getFile() != null && SequenceUtil.FILETYPE.vcf.getFileType().isType(o.getFile());
+        return o.getFile() != null && SequenceUtil.FILETYPE.bcf.getFileType().isType(o.getFile());
     }
 
     @Override
@@ -90,8 +90,6 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
             }
 
             File expectedFinalOutput = new File(ctx.getOutputDir(), outputBaseName + ".vcf.gz");
-            File expectedFinalOutputIdx = new File(expectedFinalOutput.getPath() + ".tbi");
-            boolean jobCompleted = expectedFinalOutputIdx.exists();  // this would occur if the job died during the cleanup phase
 
             File ouputVcf = runSawfishCall(ctx, filesToProcess, genome, outputBaseName);
 
@@ -150,20 +148,22 @@ private File runSawfishCall(JobContext ctx, List<File> inputs, ReferenceGenome g
                 if (vcfOutFinal.exists())
                 {
                     vcfOutFinal.delete();
-                    FileUtils.moveFile(vcfOut, vcfOutFinal);
-
-                    File targetIndex = new File(vcfOutFinal.getPath() + ".tbi");
-                    if (targetIndex.exists())
-                    {
-                        targetIndex.delete();
-                    }
+                }
+                FileUtils.moveFile(vcfOut, vcfOutFinal);
 
-                    File origIndex = new File(vcfOut.getPath() + ".tbi");
-                    if (origIndex.exists())
-                    {
-                        FileUtils.moveFile(origIndex, targetIndex);
-                    }
+                File targetIndex = new File(vcfOutFinal.getPath() + ".tbi");
+                if (targetIndex.exists())
+                {
+                    targetIndex.delete();
+                }
 
+                File origIndex = new File(vcfOut.getPath() + ".tbi");
+                if (origIndex.exists())
+                {
+                    FileUtils.moveFile(origIndex, targetIndex);
+                }
+                else
+                {
                     SequenceAnalysisService.get().ensureVcfIndex(vcfOutFinal, ctx.getLogger(), true);
                 }
             }

SequenceAnalysis/src/org/labkey/sequenceanalysis/util/SequenceUtil.java

@@ -96,6 +96,7 @@ public enum FILETYPE
         bed(Collections.singletonList(".bed"), true),
         bw(Collections.singletonList(".bw"), false),
         vcf(List.of(".vcf"), true),
+        bcf(List.of(".bcf"), true),
         gvcf(List.of(".g.vcf"), true);
 
         private final List<String> _extensions;