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Set up
$ mkdir -p $OUTDIR
Test using bam as input
$ $BLASR_EXE $DATDIR/test_bam/tiny_bam.fofn $DATDIR/lambda_ref.fasta -m 4 --out $OUTDIR/tiny_bam_in.m4
[INFO]* (glob)
[INFO]* (glob)
Check whether blasr produces identical results taking fasta sequences of the bam as input
$ $BLASR_EXE $DATDIR/test_bam/tiny_fasta.fofn $DATDIR/lambda_ref.fasta -m 4 --out $OUTDIR/tiny_fasta_in.m4
[INFO]* (glob)
[INFO]* (glob)
$ diff $OUTDIR/tiny_bam_in.m4 $OUTDIR/tiny_fasta_in.m4
Test bam in, bam out
$ $BLASR_EXE $DATDIR/test_bam/tiny_bam.fofn $DATDIR/lambda_ref.fasta --bam --out $OUTDIR/tiny_bam_in.bam --clipping subread
[INFO]* (glob)
[INFO]* (glob)
TODO: test --concordant, when pbbam API to query over ZMWs is available.
TODO: test bam with ccs reads
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