Bugfix to MergeBamAlignment

Author: bbimber

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

@@ -94,7 +94,7 @@ else if (header.getReadGroups().size() > 1)
                 FastqToSamWrapper fq = new FastqToSamWrapper(getLogger());
                 fq.setOutputDir(alignedBam.getParentFile());
                 fq.setStringency(ValidationStringency.SILENT);
-                File unmappedReadsBam = fq.execute(pair.getKey(), pair.getValue(), SAMFileHeader.SortOrder.queryname, rg);
+                File unmappedReadsBam = fq.execute(pair.getKey(), pair.getValue(), SAMFileHeader.SortOrder.unsorted, rg);
                 if (!unmappedReadsBam.exists())
                 {
                     throw new PipelineJobException("BAM file not created, expected: " + unmappedReadsBam.getPath());
@@ -121,8 +121,6 @@ else if (header.getReadGroups().size() > 1)
             params.add("--UNMAPPED_BAM");
             params.add(finalUnmappedReadsBam.getPath());
 
-            //TODO: bisulfiteSequence
-
             params.add("--REFERENCE_SEQUENCE");
             params.add(refFasta.getPath());