Convert RSII to BAM

From jchin:

Here is an example how I convert NCBI download PacBio tgz archived bax.h5 files to bam and fasta files for assembly. Hope it is useful.

for f in `ls *.tgz`; do echo tar -zxvf $f; done | parallel -j 4 &
mkdir BAX_FILES
mv *.h5 *,xml BAX_FILES/
mv *.xml BAX_FILES/
cd BAX_FILES/
for f in `ls *.bas.h5`; do echo bax2bam $f ; done | parallel -j 8 &
mkdir ../BAM_FILES
mv *.bam *.pbi ../BAM_FILES/
cd ..
cd BAM_FILES/
for f in `ls *.bam`; do echo bam2fasta -u $f -o ${f:0:61}; done | parallel -j 8