Hi, I used blasr aligner to align a pacbio dataset against a reference. I used *.bax.h5 files for the alignemnt. Since there were three *.bax.h5 file for a single sample I used the command as follows:

    blasr m160128_145513_42215_c100901562550000001823208404291605_s1_p0.1.bax.h5 m160128_145513_42215_c100901562550000001823208404291605_s1_p0.1.bax.h5 m160128_145513_42215_c100901562550000001823208404291605_s1_p0.1.bax.h5 query.fasta -sam  -unaligned unaligned.reads -nproc 8 -out output.sam

I converted the sam to bam and sorted it. Now, when I check the bam file for the counts of read mapped/unmapped, I get something like this:

    samtools view -c -F 4 output.sorted.bam 

    12978

but when I use a different approach of counting reads I get 3 different values:

    samtools view -F 4 output.sorted.bam | wc

    12978  298494 9212184

I am not able to understand if these 3 values belong to individual *.bax.h5 I originally used in the mapping or this something else? 

Or 

is there any other way to use 3 bax.h5 file together in the same mapping step?

Thanks
`man wc`

12978 is the number of lines and exactly what `samtools view -c ...` reported.

298494 is the number of words. This is useless.

9212184 is the number of characters. This is useless.

You probably wanted `wc -l` rather than just `wc`.