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Set up
$ . $TESTDIR/setup.sh
Set up the executable: pls2fasta.
$ EXEC=$TESTDIR/../pls2fasta
Test pls2fasta
Condition: the order of region tables do not match the order bax.h5 files.
$ $EXEC $DATDIR/test_pls2fasta.fofn $OUTDIR/test_pls2fasta.fa -regionTable $DATDIR/test_pls2fasta_rgn.fofn -trimByRegion
[INFO] * [pls2fasta] started. (glob)
[INFO] * [pls2fasta] ended. (glob)
Test pls2fasta output fastq
$ $EXEC $DATDIR/ecoli_lp.fofn $OUTDIR/test_pls2fasta_ecoli.fq -trimByRegion -fastq
[INFO] * [pls2fasta] started. (glob)
[INFO] * [pls2fasta] ended. (glob)
$ echo $?
0
$ diff $OUTDIR/test_pls2fasta_ecoli.fq $STDDIR/test_pls2fasta_ecoli.fq
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