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Set up
$ mkdir -p $OUTDIR
Test blasr with *.fofn input
# $ rm -rf $OUTDIR/lambda_bax.m4
# $ $BLASR_EXE $DATDIR/lambda_bax.fofn $DATDIR/lambda_ref.fasta -m 4 --out lambda_bax_tmp.m4 --nproc 15 --minMatch 14
# [INFO]* (glob)
# [INFO]* (glob)
# $ sort lambda_bax_tmp.m4 > $OUTDIR/lambda_bax.m4
# $ diff $OUTDIR/lambda_bax.m4 $STDDIR/lambda_bax.m4
# This test takes a long time, use a subset instad.
$ rm -rf $OUTDIR/lambda_bax_subset.m4
$ $BLASR_EXE $DATDIR/lambda_bax.fofn $DATDIR/lambda_ref.fasta -m 4 --out $OUTDIR/lambda_bax_tmp_subset.m4 --nproc 15 --minMatch 14 --holeNumbers 1--1000 --sa $DATDIR/lambda_ref.sa
[INFO]* (glob)
[INFO]* (glob)
$ sort $OUTDIR/lambda_bax_tmp_subset.m4 > $OUTDIR/lambda_bax_subset.m4
$ diff $OUTDIR/lambda_bax_subset.m4 $STDDIR/lambda_bax_subset.m4
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