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Set up
$ mkdir -p $OUTDIR
$ NAME=test_hitpolicy
$ DATDIR=$DATDIR/$NAME
$ OUTDIR=$OUTDIR/$NAME
$ STDDIR=$STDDIR/$NAME
$ mkdir -p $OUTDIR
$ I=$DATDIR/tiny_bam.fofn
$ R=$DATDIR/test_hitpolicy_target.fa
$ O=$OUTDIR/hitpolicy_all.m4
$ X=$STDDIR/hitpolicy_all.m4
Test hitpolicy all
$ $BLASR_EXE $I $R --out $O -m 4 --hitPolicy all
[INFO]* (glob)
[INFO]* (glob)
$ echo $?
0
$ wc -l $O | cut -f 1 -d ' '
683
Test hitpolicy allbest
$ O=$OUTDIR/hitpolicy_allbest.m4
$ X=$STDDIR/hitpolicy_allbest.m4
$ $BLASR_EXE $I $R --out $O -m 4 --hitPolicy allbest && sort $O > $TMP1 && mv $TMP1 $O
[INFO]* (glob)
[INFO]* (glob)
$ echo $?
0
$ sort $O > $TMP1 && mv $TMP1 $O
$ diff $O $X && echo $?
0
Test hitpolicy random
$ O=$OUTDIR/hitpolicy_random.m4
$ O2=$OUTDIR/hitpolicy_random_2.m4
$ X=$STDDIR/hitpolicy_random.m4
$ $BLASR_EXE $I $R --out $O -m 4 --hitPolicy random --randomSeed 1
[INFO]* (glob)
[INFO]* (glob)
$ $BLASR_EXE $I $R --out $O2 -m 4 --hitPolicy random --randomSeed 1
[INFO]* (glob)
[INFO]* (glob)
$ sort $O > $TMP1 && mv $TMP1 $O
$ sort $O2 > $TMP2 && mv $TMP2 $O2
$ diff $O $O2 && echo $?
0
Test hitpolicy randombest bam inputs, nproc > 1, fixed seed
$ O=$OUTDIR/hitpolicy_randombest_bam_in.m4
$ O2=$OUTDIR/hitpolicy_randombest_bam_in_2.m4
$ X=$STDDIR/hitpolicy_randombest_bam_in.m4
$ $BLASR_EXE $I $R --out $O -m 4 --hitPolicy randombest --randomSeed 1 --nproc 10
[INFO]* (glob)
[INFO]* (glob)
$ $BLASR_EXE $I $R --out $O2 -m 4 --hitPolicy randombest --randomSeed 1 --nproc 10
[INFO]* (glob)
[INFO]* (glob)
$ sort $O > $TMP1 && mv $TMP1 $O
$ sort $O2 > $TMP1 && mv $TMP1 $O2
$ diff $O $O2 && echo $?
0
Test hitpolicy randombest bax inputs, nproc > 1, fixed seed
$ I=$DATDIR/tiny_bax.fofn
$ O=$OUTDIR/hitpolicy_randombest_bax_in.m4
$ X=$STDDIR/hitpolicy_randombest_bax_in.m4
$ $BLASR_EXE $I $R --out $O -m 4 --hitPolicy randombest --randomSeed 1 --nproc 10
[INFO]* (glob)
[INFO]* (glob)
$ sort $O > $TMP1 && mv $TMP1 $O
$ diff $O $X && echo $?
0
Test hitpolicy randombest fasta inputs, nproc > 1, fixed seed
$ I=$DATDIR/tiny_fasta.fofn
$ O=$OUTDIR/hitpolicy_randombest_fasta_in.m4
$ X=$STDDIR/hitpolicy_randombest_fasta_in.m4
$ $BLASR_EXE $I $R --out $O -m 4 --hitPolicy randombest --randomSeed 1 --nproc 10
[INFO]* (glob)
[INFO]* (glob)
$ sort $O > $TMP1 && mv $TMP1 $O
$ diff $O $X && echo $?
0
Test hitpolicy leftmost
$ O=$OUTDIR/hitpolicy_leftmost.m4
$ X=$STDDIR/hitpolicy_leftmost.m4
$ $BLASR_EXE $I $R --out $O -m 4 --hitPolicy leftmost --nproc 10
[INFO]* (glob)
[INFO]* (glob)
$ # target is lambda x 6, leftmost -> only map to the very first x.
$ awk '$10 > 48502 {print}' $O |wc -l
0
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