Set up 
  $ . $TESTDIR/setup.sh

Set up the executable: swMather.
  $ EXEC=$TESTDIR/../swMatcher

Define tmporary files
  $ TMP1=$OUTDIR/$$.tmp.out
  $ TMP2=$OUTDIR/$$.tmp.stdout

Make OUTDIR
  $ mkdir -p $OUTDIR

  $ FA=$DATDIR/ecoli_subset.fasta
  $ $EXEC $FA $FA 10 -local  > $OUTDIR/swmatcher.out
  $ echo $?
  0
  $ diff $OUTDIR/swmatcher.out $STDDIR/swmatcher.stdout