1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
|
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: sdpMatcher.
$ EXEC=$TESTDIR/../sdpMatcher
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/sdpMatcher.out
$ echo $?
0
$ diff $OUTDIR/sdpMatcher.out $STDDIR/sdpMatcher.stdout
|
