New GATK default behavior is to output all @Output annotations to stdout by default.  This was happening with the option VCF output.  Changed the defaultToStdout to false
fixed describe to pull tags as well
changed output of strand contingency table to use same reads as used in the strand specific lod scores.  the overall lod score and the old contingency table used the same data.  However, if there was a fragment  with overlapping reads this would be counted once in the overall lod score and old contingency table (to not double count the fragment) but twice in the strand lod score calculation.  This became confusing, for example, if we have one fragment with overlapping reads (with reference base).  The old table would read (1,0,0,0) but the new one would read (1,1,0,0).  This is important because the site might pass the strand specific lod test, but the old contingency table might show zero reads in one direction, although one read in each direction was considered in the strand specific lod score.