Re: [Samtools-help] samtools view -F/-f multiple times

[James B. <jk...@sa...>]

On Wed, Jun 22, 2016 at 11:42:08AM +0100, Dario Beraldi wrote:
> samtools view -F 128 -F 16 ...
> 
> is the same as
> 
> samtools view -F 144 ...
> 
> Is this behaviour documented somewhere and intentional?

It is intentional, but I don't think it is documented anywhere.

The field is a bit field, and documented as such, so 144 is considered
as 128 OR 16 rather than 128+16.  This in turn means -F 128 -F 16 -F
16 or -F 144 -F 16 will still be 144 and not 160, so there is some
built in safety there.

> I'm asking because I have some scripts that rely on this behaviour so I
> would like to know whether it's going to be supported or changed.

The code to make it work as repeatable bit-fields is trivial (just one
line extra byte[1] of source code for each of -f and -F) so there
isn't any logical reason I can think of why it would need to be
replaced.  I'd even go as far to say there is a beauty and elegance in
its simplicity; not something you'll often here me say about
samtools. :-)

James

[1] The '|' character.

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James Bonfield (jk...@sa...) | Hora aderat briligi. Nunc et Slythia Tova
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https://sf.net/projects/staden/   | Momiferique omnes exgrabure Rathi. 


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