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Set up directories
$ CURDIR=$TESTDIR
$ REMOTEDIR=/pbi/dept/secondary/siv/testdata/BlasrTestData/ctest
$ DATDIR=$REMOTEDIR/data
$ OUTDIR=$CURDIR/out
$ STDDIR=$REMOTEDIR/stdout
Set up the executable: sawriter.
$ EXEC=$TESTDIR/../sawriter
Define tmporary files
$ TMP1=$OUTDIR/$$.tmp.out
$ TMP2=$OUTDIR/$$.tmp.stdout
Make OUTDIR
$ mkdir -p $OUTDIR
$ $EXEC $OUTDIR/ecoli_larsson.sa $DATDIR/ecoli_reference.fasta -blt 11 -larsson
$ echo $?
0
$ $EXEC $OUTDIR/ecoli_welter.sa $DATDIR/ecoli_reference.fasta -blt 11 -welter 2>&1 >$OUTDIR/sawriter.log
$ echo $?
0
$ md5sum $OUTDIR/ecoli_larsson.sa |cut -f 1 -d ' '
e23b6afe6ddd74b2656e36bf93f6840c
$ md5sum $OUTDIR/ecoli_welter.sa |cut -f 1 -d ' '
e23b6afe6ddd74b2656e36bf93f6840c
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