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Set up
$ mkdir -p $OUTDIR
Test generating bam output
Input is bam, clipping=soft and subread should produce identical results
$ $BLASR_EXE $DATDIR/test_bam/tiny_bam.fofn $DATDIR/lambda_ref.fasta --bam --out $OUTDIR/tiny_bam_in_soft.bam --clipping soft
[INFO]* (glob)
[INFO]* (glob)
$ $BLASR_EXE $DATDIR/test_bam/tiny_bam.fofn $DATDIR/lambda_ref.fasta --bam --out $OUTDIR/tiny_bam_in_subread.bam --clipping subread
[INFO]* (glob)
[INFO]* (glob)
$ $SAMTOOLS_EXE view $OUTDIR/tiny_bam_in_soft.bam | sed -n '6,$p' > $TMP1.bam_in_soft
$ $SAMTOOLS_EXE view $OUTDIR/tiny_bam_in_subread.bam | sed -n '6,$p' > $TMP2.bam_in_subread
$ diff $TMP1.bam_in_soft $TMP2.bam_in_subread
Test if bam cigar strings are correct
$ head -2 $TMP1.bam_in_soft |cut -f 6
25=1I28=1I41=1I5=1D6=1X12=1I15=1I2=1I16=1D10=1I11=1I74=1D12=1D7=3I4=1I6=1D1=2D14=1D16=1I8=1D4=1D5=1D20=1I3=1I10=1I37=1I13=1I25=1I15=1I7=1I11=1I3=2I1=1I16=1I6=1I8=1I11=1X1=1I5=1I56=1I17=
28=1D7=1I1=1I9=2I12=1I3=1D13=1I15=1I2=1X49=1I19=1I14=1I5=1D17=1D20=1D86=1I21=1I9=1I24=1I6=1I1=1I2=1D11=1D4=1D3=1D31=1D6=1I6=1I9=1I57=2I24=1I26=1I8=1I43=1S
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