Dear samtools developers:
I am now using samtools-1.3. I have some questions for the options in
command samtools view. There are nine CIGAR operations, and the sum of
lengths of these operations equal the length of query sequence. So no
matter the value of option m, it will output all the alignment. There is no
need for this option. And the option f,what do you mean by all bits set in
*INT* present in the FLAG field? To my knowledge, different bits have
different value, and it is impossible to find alignments that all bits set
in the same value. I tried hard to understand the options -m, -f, -B for
command samtools view, but I still do not figure out their meanings. If
possible, could you please show me an example for these options? Thanks
very much for your time.
Best
Jing
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