1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
|
Set up
$ mkdir -p $OUTDIR
Test blasr with input bam which has:
(1) insertionQV, deletionQV, deletionTag, substitutionQV, substitutionTag
(2) insertionQV, deletionQV, deletionTag
(3) no QV
and then check if output is determined.
(1)
$ name=iq-dq-sub
$ infile=$DATDIR/test_bam/$name.subreads.bam
$ outfile=$OUTDIR/$name.m4
$ stdfile=$STDDIR/$name.m4
$ rm -f $outfile
$ $BLASR_EXE $infile $DATDIR/lambda_ref.fasta -m 4 --out $outfile && echo $?
[INFO]* (glob)
[INFO]* (glob)
0
$ sort $outfile > $outfile.tmp && mv $outfile.tmp $outfile
$ diff $outfile $stdfile
(2)
$ name=iq-dq
$ infile=$DATDIR/test_bam/$name.subreads.bam
$ outfile=$OUTDIR/$name.m4
$ stdfile=$STDDIR/$name.m4
$ rm -f $outfile
$ $BLASR_EXE $infile $DATDIR/lambda_ref.fasta -m 4 --out $outfile && echo $?
[INFO]* (glob)
[INFO]* (glob)
0
$ sort $outfile > $outfile.tmp && mv $outfile.tmp $outfile
$ diff $outfile $stdfile
(3)
$ name=no-iq-dq
$ infile=$DATDIR/test_bam/$name.subreads.bam
$ outfile=$OUTDIR/$name.m4
$ stdfile=$STDDIR/$name.m4
$ rm -f $outfile
$ $BLASR_EXE $infile $DATDIR/lambda_ref.fasta -m 4 --out $outfile && echo $?
[INFO]* (glob)
[INFO]* (glob)
0
$ sort $outfile > $outfile.tmp && mv $outfile.tmp $outfile
$ diff $outfile $stdfile
|
