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Set up directories
$ . $TESTDIR/setup.sh
Set up the executable: samtom4.
$ EXEC=$TESTDIR/../samtom4
#Test samtom4 with a *.sam file generated by blasr from a fofn
$ OUTFILE=$OUTDIR/lambda_bax.m4
#STDFILE has been generated by blasr -m 4 && sort
$ STDFILE=$STDDIR/lambda_bax.m4
$ TMPFILE=test_samtom4_2.tmp
$ rm -rf $OUTFILE $TMPFILE
$ $EXEC $DATDIR/lambda_bax.sam $DATDIR/lambda_ref.fasta $TMPFILE
$ sort $TMPFILE > $OUTFILE
$ diff $OUTFILE $STDFILE
$ rm $TMPFILE
#Test samtom4 with a *.sam file generated by blasr with -noSplitSubreads from a fofn
$ OUTFILE=$OUTDIR/lambda_bax_noSplitSubreads.m4
#STDFILE has been generated by blasr -m 4 && sort
$ STDFILE=$STDDIR/lambda_bax_noSplitSubreads.m4
$ TMPFILE=test_samtom4_3.tmp
$ rm -rf $OUTFILE $TMPFILE
$ $EXEC $DATDIR/lambda_bax_noSplitSubreads.sam $DATDIR/lambda_ref.fasta $TMPFILE
$ sort $TMPFILE > $OUTFILE
$ diff $OUTFILE $STDFILE
$ rm $TMPFILE
#Test samtom4 with a *.sam file generated by blasr.
$ OUTFILE=$OUTDIR/ecoli_samtom4.m4
#STDFILE has been generated by blasr -m 4 && sort
$ STDFILE=$STDDIR/ecoli_sorted.m4
$ TMPFILE=$OUTDIR/test_samtom4_4.tmp
$ rm -rf $OUTFILE $TMPFILE
$ $EXEC $DATDIR/ecoli.sam $DATDIR/ecoli_reference.fasta $OUTFILE -useShortRefName
$ sort -n $OUTFILE > $TMPFILE
$ diff $TMPFILE $STDFILE
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