Re: [Samtools-help] Filter reads with multiple flags - samtools view

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

On Mon, Feb 28, 2011 at 11:59:32AM +0000, Peter wrote:
> I've never tried, but in that case try combining the desired flags, 0x02 plus/or
> 0x08 is 0x0A (in binary, 2+8=10), so I'd expect -f 0x0A will do what you want.

Sometimes you want to filter by either-OR. So either 2 or 8 (or
both). In that case "(flags & 10) != 0" is a suitable boolean
condition.

Othertimes we want to filter by AND. So 2 and 8 must both be set,
implying "(flags & 10) == 10" is a suitable boolean.

The latter method is how samtools works and is probably what most
users typically want/expect. The documentation for -f states "Only
output alignments with all bits in INT present in the FLAG field" - ie
it's an explicit AND operation and not OR.

I don't know if it's possible too do the first OR case, if that is
indeed what you wanted.  The original poster mentioned trying multiple
-f parameters, which would be a reasonable way to implement an OR
mechanism.

-- 
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  A Staden Package developer:     | Et Borogovorum mimzebant undique formae,
https://sf.net/projects/staden/   | Momiferique omnes exgrabure Rathi. 


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