N Remover Tool

[dstreett]

Returns the longest sequence without Ns

[bioSandMan]

The nremover part is working. I need to incorporate the changes into the code with new IO.

[dstreett]

When you are ready for it to be looked over, please do a pull request. If you have any questions about that, let me know and I will be happy to help out.

Also, be sure you have a header file with the core functionality that you have unit test for.

[msettles]

Has anything been written down algorithmically for these tools? What are the assumptions, what is the goal, what is the alg (where was it derived from)

Matt

From: David Streett notifications@github.com
Reply-To: ibest/HTStream reply@reply.github.com
Date: Wednesday, September 7, 2016 at 6:32 AM
To: ibest/HTStream HTStream@noreply.github.com
Subject: Re: [ibest/HTStream] N Remover Tool (#4)

When you are ready for it to be looked over, please do a pull request. If you have any questions about that, let me know and I will be happy to help out.

Also, be sure you have a header file with the core functionality that you have unit test for.

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[dstreett]

Hey @msettles,

Good to hear from you. :)

So, N remover will be a simple O(N) algorithm that will loop through the entire read and get the longest non-n chunk possible. If this non-n chunk is greater than the minimum length requirement it is kept. If it isn't it is discarded. If it is a PE and only R1 is discarded, and the stranded option is set, R2 will become a SE RC read. Otherwise, the stand alone read will stay the same if its mate is discarded. Sound good? Did that answer your question or did I miss something?

I'm going to hop on over to the Poly AT question #26 stuff now and talk about sliding windows. :)

[joe-angell]

How about we put that in the help text or README?

On Wed, Sep 7, 2016 at 10:14 AM, David Streett notifications@github.com
wrote:

Hey @msettles https://github.com/msettles,

Good to hear from you. :)

So, N remover will be a simple O(N) algorithm that will loop through the
entire read and get the longest non-n chunk possible. If this non-n chunk
is greater than the minimum length requirement it is kept. If it isn't it
is discarded. If it is a PE and only R1 is discarded, and the stranded
option is set, R2 will become a SE RC read. Otherwise, the stand alone read
will stay the same if its mate is discarded. Sound good? Did that answer
your question or did I miss something?

I'm going to hop on over to the Poly AT question #26
https://github.com/ibest/HTStream/issues/26 stuff now and talk about
sliding windows. :)

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You are receiving this because you are subscribed to this thread.
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cell: (720) 260-2190

[msettles]

Yes help text / Readme and that was a general question for ALL the algs, that way concept folks like myself (who don’t have time to dig into code) can look through and poke any holes that might be present!

Great description, thanks, and can’t think of any holes at the moment ;)

Matt

From: Joe Angell notifications@github.com
Reply-To: ibest/HTStream reply@reply.github.com
Date: Wednesday, September 7, 2016 at 10:38 AM
To: ibest/HTStream HTStream@noreply.github.com
Cc: Matt Settles mattsettles@gmail.com, Mention mention@noreply.github.com
Subject: Re: [ibest/HTStream] N Remover Tool (#4)

How about we put that in the help text or README?

On Wed, Sep 7, 2016 at 10:14 AM, David Streett notifications@github.com
wrote:

Hey @msettles https://github.com/msettles,

Good to hear from you. :)

So, N remover will be a simple O(N) algorithm that will loop through the
entire read and get the longest non-n chunk possible. If this non-n chunk
is greater than the minimum length requirement it is kept. If it isn't it
is discarded. If it is a PE and only R1 is discarded, and the stranded
option is set, R2 will become a SE RC read. Otherwise, the stand alone read
will stay the same if its mate is discarded. Sound good? Did that answer
your question or did I miss something?

I'm going to hop on over to the Poly AT question #26
https://github.com/ibest/HTStream/issues/26 stuff now and talk about
sliding windows. :)

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You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
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.

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Joe Angell
cell: (720) 260-2190

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[dstreett]

Yep, everything will be in 3 locations. Readme, --help (-h), and on the gitio pages and I will reuse them in my thesis . . . after a bit more development on the applications themselves. :)

[bioSandMan]

@dstreett

I didn’t realize the stranded part. Can you explain what an "SE RC" read is? What does “RC” stand for?

Thanks