Add sorting to FixMateInformation output

Author: bbimber

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/AbstractCommandWrapper.java

@@ -263,6 +263,11 @@ protected void setLogLevel(Level logLevel)
         _logLevel = logLevel;
     }
 
+    public Level getLogLevel()
+    {
+        return _logLevel;
+    }
+
     public void setWarnNonZeroExits(boolean warnNonZeroExits)
     {
         _warnNonZeroExits = warnNonZeroExits;

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/StarWrapper.java

@@ -4,6 +4,7 @@
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.SystemUtils;
+import org.apache.log4j.Level;
 import org.apache.log4j.Logger;
 import org.jetbrains.annotations.Nullable;
 import org.json.JSONObject;
@@ -489,7 +490,11 @@ public void logVersionString() throws PipelineJobException
         args.add(getExe(false).getPath());
         args.add("--version");
 
-        String version = executeWithOutput(args);
-        getLogger().info("STAR version: " + version);
+        getLogger().info("STAR version: ");
+
+        Level origLavel = getLogLevel();
+        setLogLevel(Level.INFO);
+        execute(args);
+        setLogLevel(origLavel);
     }
 }

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/bampostprocessing/FixMateInformationStep.java

@@ -1,5 +1,6 @@
 package org.labkey.sequenceanalysis.run.bampostprocessing;
 
+import htsjdk.samtools.SAMFileHeader;
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.sequenceanalysis.model.Readset;
 import org.labkey.api.sequenceanalysis.pipeline.BamProcessingOutputImpl;
@@ -11,8 +12,10 @@
 import org.labkey.api.sequenceanalysis.pipeline.ReferenceGenome;
 import org.labkey.api.sequenceanalysis.run.AbstractCommandPipelineStep;
 import org.labkey.sequenceanalysis.run.util.FixMateInformationWrapper;
+import org.labkey.sequenceanalysis.util.SequenceUtil;
 
 import java.io.File;
+import java.io.IOException;
 
 /**
  * User: bimber
@@ -48,7 +51,16 @@ public BamProcessingStep.Output processBam(Readset rs, File inputBam, ReferenceG
 
         File outputBam = new File(outputDirectory, FileUtil.getBaseName(inputBam) + ".fixmate.bam");
         output.addIntermediateFile(outputBam);
-        output.setBAM(getWrapper().executeCommand(inputBam, outputBam));
+
+        try
+        {
+            SAMFileHeader.SortOrder so = SequenceUtil.getBamSortOrder(inputBam);
+            output.setBAM(getWrapper().executeCommand(inputBam, outputBam, so));
+        }
+        catch (IOException e)
+        {
+            throw new PipelineJobException(e);
+        }
 
         return output;
     }

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

@@ -1,5 +1,6 @@
 package org.labkey.sequenceanalysis.run.util;
 
+import htsjdk.samtools.SAMFileHeader;
 import org.apache.log4j.Logger;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.pipeline.PipelineJobException;
@@ -23,7 +24,7 @@ public FixMateInformationWrapper(@Nullable Logger logger)
     /**
      * If the output file is null, the original will be deleted and replaced by the fixed BAM
      */
-    public File executeCommand(File inputFile, @Nullable File outputFile) throws PipelineJobException
+    public File executeCommand(File inputFile, @Nullable File outputFile, @Nullable SAMFileHeader.SortOrder so) throws PipelineJobException
     {
         getLogger().info("Fixing Mate Information: " + inputFile.getPath());
 
@@ -33,6 +34,12 @@ public File executeCommand(File inputFile, @Nullable File outputFile) throws Pip
         if (outputFile != null)
             params.add("OUTPUT=" + outputFile.getPath());
 
+        if (so != null)
+        {
+            params.add("-SO");
+            params.add(so.name());
+        }
+
         execute(params);
 
         File expectedOut = outputFile == null ? inputFile : outputFile;