Merge remote-tracking branch 'origin/develop' into fb_fileNameAudit

Author: labkey-susanh

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

@@ -49,37 +49,16 @@ public Output performAnalysisPerSampleRemote(Readset rs, File inputBam, Referenc
     {
         AnalysisOutputImpl output = new AnalysisOutputImpl();
 
-        File inputFile = inputBam;
-        if (SequenceUtil.FILETYPE.cram.getFileType().isType(inputFile))
-        {
-            CramToBam samtoolsRunner = new CramToBam(getPipelineCtx().getLogger());
-            File bam = new File(getPipelineCtx().getWorkingDirectory(), inputFile.getName().replaceAll(".cram$", ".bam"));
-            File bamIdx = new File(bam.getPath() + ".bai");
-            if (!bamIdx.exists())
-            {
-                samtoolsRunner.convert(inputFile, bam, referenceGenome.getWorkingFastaFile(), SequencePipelineService.get().getMaxThreads(getPipelineCtx().getLogger()));
-                new SamtoolsIndexer(getPipelineCtx().getLogger()).execute(bam);
-            }
-            else
-            {
-                getPipelineCtx().getLogger().debug("BAM index exists, will not re-convert CRAM");
-            }
-
-            inputFile = bam;
-
-            output.addIntermediateFile(bam);
-            output.addIntermediateFile(bamIdx);
-        }
-
         List<String> args = new ArrayList<>();
         args.add(getExe().getPath());
         args.add("discover");
 
         args.add("--bam");
-        args.add(inputFile.getPath());
+        args.add(inputBam.getPath());
 
+        // NOTE: sawfish stores the absolute path of the FASTA in the output JSON, so dont rely on working copies:
         args.add("--ref");
-        args.add(referenceGenome.getWorkingFastaFile().getPath());
+        args.add(referenceGenome.getSourceFastaFile().getPath());
 
         File svOutDir = new File(outputDir, "sawfish");
         args.add("--output-dir");
@@ -123,41 +102,4 @@ private File getExe()
     {
         return SequencePipelineService.get().getExeForPackage("SAWFISHPATH", "sawfish");
     }
-
-    private static class CramToBam extends SamtoolsRunner
-    {
-        public CramToBam(Logger log)
-        {
-            super(log);
-        }
-
-        public void convert(File inputCram, File outputBam, File fasta, @Nullable Integer threads) throws PipelineJobException
-        {
-            getLogger().info("Converting CRAM to BAM");
-
-            execute(getParams(inputCram, outputBam, fasta, threads));
-        }
-
-        private List<String> getParams(File inputCram, File outputBam, File fasta, @Nullable Integer threads)
-        {
-            List<String> params = new ArrayList<>();
-            params.add(getSamtoolsPath().getPath());
-            params.add("view");
-            params.add("-b");
-            params.add("-T");
-            params.add(fasta.getPath());
-            params.add("-o");
-            params.add(outputBam.getPath());
-
-            if (threads != null)
-            {
-                params.add("-@");
-                params.add(String.valueOf(threads));
-            }
-
-            params.add(inputCram.getPath());
-
-            return params;
-        }
-    }
 }

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

@@ -120,9 +120,6 @@ private File runSawfishCall(JobContext ctx, List<File> inputs, ReferenceGenome g
                 args.add(String.valueOf(maxThreads));
             }
 
-            args.add("--ref");
-            args.add(genome.getWorkingFastaFile().getPath());
-
             for (File sample : inputs)
             {
                 args.add("--sample");
@@ -177,7 +174,7 @@ private File runSawfishCall(JobContext ctx, List<File> inputs, ReferenceGenome g
 
         private File getExe()
         {
-            return SequencePipelineService.get().getExeForPackage("PBSVPATH", "pbsv");
+            return SequencePipelineService.get().getExeForPackage("SAWFISHPATH", "sawfish");
         }
     }
 }

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/CramToBamWrapper.java

@@ -0,0 +1,47 @@
+package org.labkey.sequenceanalysis.run.util;
+
+import org.apache.logging.log4j.Logger;
+import org.jetbrains.annotations.Nullable;
+import org.labkey.api.pipeline.PipelineJobException;
+import org.labkey.api.sequenceanalysis.pipeline.SamtoolsRunner;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+
+public class CramToBamWrapper extends SamtoolsRunner
+{
+    public CramToBamWrapper(Logger log)
+    {
+        super(log);
+    }
+
+    public void convert(File inputCram, File outputBam, File fasta, @Nullable Integer threads) throws PipelineJobException
+    {
+        getLogger().info("Converting CRAM to BAM");
+
+        execute(getParams(inputCram, outputBam, fasta, threads));
+    }
+
+    private List<String> getParams(File inputCram, File outputBam, File fasta, @Nullable Integer threads)
+    {
+        List<String> params = new ArrayList<>();
+        params.add(getSamtoolsPath().getPath());
+        params.add("view");
+        params.add("-b");
+        params.add("-T");
+        params.add(fasta.getPath());
+        params.add("-o");
+        params.add(outputBam.getPath());
+
+        if (threads != null)
+        {
+            params.add("-@");
+            params.add(String.valueOf(threads));
+        }
+
+        params.add(inputCram.getPath());
+
+        return params;
+    }
+}