Add a 'shift' tool.

[arq5x]

shift should move an interval left or right by either a fixed number of bases or a specific fraction of a chromosome.

[ttriche]

any news on this before I write it? :-)

[arq5x]

Unfortunately, I haven't gotten around to this yet. Sorry!

[ttriche]

nevermind, it looks like bedtools slop does this anyhow (at least in 2.2.0)

thanks!

Statistics is the grammar of science.
Karl Pearson http://en.wikipedia.org/wiki/The_Grammar_of_Science

On Wed, Sep 17, 2014 at 1:36 PM, Aaron Quinlan notifications@github.com
wrote:

Unfortunately, I haven't gotten around to this yet. Sorry!

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Reply to this email directly or view it on GitHub
#40 (comment).

[arq5x]

That is a slightly different op...

[ttriche]

eh, I may just use pandas on the bedGraph then ;-)

Statistics is the grammar of science.
Karl Pearson http://en.wikipedia.org/wiki/The_Grammar_of_Science

On Wed, Sep 17, 2014 at 2:22 PM, Aaron Quinlan notifications@github.com
wrote:

That is a slightly different op...

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#40 (comment).

[ttriche]

Actually scratch that, I think I will go ahead and pick at the C++ data structures to make it fast and stream-capable. Why not do it right, (more or less) once and for all.

[ttriche]

It is better to do so with the bedtools2 repository though, yes?

[arq5x]

The code in the slop tool will get you 90% of the way.

[arq5x]

Indeed.

[brentp]

seems like this could just be a new option in slop.

[arq5x]

Perhaps, but I see them as fundamentally different. Slop maintains the "center" of the interval and extends the ends in both or either direction. The purpose of shift is to move the interval left or right, but not change its size.

[arq5x]

I think I must be a bit bad at choosing verbs for the tools, as some of these cause confusion for many!

[brentp]

could be fun to think of the verb first, then decide what the tool will do:

bedtools cork

bedtools sanction

bedtools advise

etc.

[arq5x]

I like the way you think, sir.