Add Pileup-->Read Converter about adam HOT 13 CLOSED

Is anyone working on this?

from adam.

Yes, paging @ananth-pallaseni...

from adam.

The code for this is almost done, just testing and fixing isssues

from adam.

@fnothaft did this ever go anywhere / have anything relevant for it checked in?

from adam.

Yes, we have work in a fork, will hopefully come to master soon.

Timothy Danford [email protected] wrote:

@fnothaft did this ever go anywhere / have anything relevant for it checked in?

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@fnothaft did this ever go anywhere / have anything relevant for it checked in?

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Reply to this email directly or view it on GitHub.

from adam.

Sounds good -- just checking.

from adam.

@fnothaft just checking in again -- is there still work on this in a branch somewhere, outstanding?

from adam.

I don't think this will be as useful as I once thought it'd be. Closing for now.

from adam.

Well, hold on, what's the story? Do we have a converter? Do we not need one? Something else? (Sorry, I just want to make it clear in the thread, why this original issue isn't a going concern anymore.)

from adam.

@tdanford there's been some work on it, but it turns out that it's more difficult to do than we'd expected, and the functionality isn't as useful as we expected. Essentially, we're 50-75% of the way towards having a converter, but it's not clear that we need one, and we'll probably want to make significant changes to the pileup format soon to address performance.

from adam.

Let's leave this issue open then, and update its top-level title and description when we have a better understanding of what we need. Or mark it as a duplicate and close it with a pointer to a better issue, if one comes along.

It seems clear to me that this is useful functionality though, converting sets of Reads to some pileup-like model efficiently is definitely an important use-case.

from adam.

It seems clear to me that this is useful functionality though, converting sets of Reads to some pileup-like model efficiently is definitely an important use-case.

This is the reverse use-case --> e.g., converting pileups back into reads. We already have reads-->pileups, but it needs performance tuning.

from adam.

Oh, jeez -- totally misread the arrow.

Yeah, okay, close away.

from adam.