Add saa=t to bbmap

Author: bbimber

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

@@ -256,6 +256,9 @@ public File doAlignment(File inputFastq1, @Nullable File inputFastq2, File outpu
         args.add("secondary=t");
         args.add("ssao=t");
 
+        // NOTE: this will increase BAM size. Consider whether really needed:
+        args.add("saa=t");
+
         // CONSIDER: mappedonly=f If true, treats 'out' like 'outm'
         // CONSIDER: outu=<file> Write only unmapped reads to this file.  Does not include unmapped paired reads with a mapped mate.
         File outputSam = new File(outputDirectory, basename + ".bbmap.sam");