Migrate preprocessing stages out of ADAM #598

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fnothaft opened this Issue Mar 1, 2015 · 4 comments

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fnothaft commented Mar 1, 2015

I propose migrating the duplicate marker, BQSR engine, and indel realigner out of ADAM. I would suggest migrating them into avocado; @massie had also suggested migrating them into a repository or project submodule dedicated to pre-processing stages.

@fnothaft fnothaft added this to the 0.17.0 milestone Mar 1, 2015

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fnothaft Mar 1, 2015

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I suggest migrating them into avocado so that we'll have a single project that goes from reads->variant calls, but am open to suggestions.

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fnothaft commented Mar 1, 2015

I suggest migrating them into avocado so that we'll have a single project that goes from reads->variant calls, but am open to suggestions.

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tdanford Mar 1, 2015

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I vote for avocado, but I'm fine with either one.

(Note, in the branch in avocado I have for mutect, I've also included other pre-processing steps. It's convenient, and it'd be nice if avocado included "necessary pre-processing steps" too.)

I think the only exception to this might be the mark duplicates implementation -- I believe that that's a pre-processing step for some ChIP-seq (i.e. non-variant-calling) pipelines too.

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tdanford commented Mar 1, 2015

I vote for avocado, but I'm fine with either one.

(Note, in the branch in avocado I have for mutect, I've also included other pre-processing steps. It's convenient, and it'd be nice if avocado included "necessary pre-processing steps" too.)

I think the only exception to this might be the mark duplicates implementation -- I believe that that's a pre-processing step for some ChIP-seq (i.e. non-variant-calling) pipelines too.

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laserson Mar 1, 2015

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I vote avocado for now as well. And either Avocado will grow into other applications/uses, or we can restructure in the future as well.

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laserson commented Mar 1, 2015

I vote avocado for now as well. And either Avocado will grow into other applications/uses, or we can restructure in the future as well.

@fnothaft fnothaft modified the milestones: 0.18.0, 0.17.0 May 31, 2015

@fnothaft fnothaft modified the milestones: 1.0.0, 0.17.1 Aug 20, 2015

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fnothaft Jul 20, 2016

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I'm going to close this. I think that with recent changes to refactor the RDD package and to privatize code, this effort would now be unnecessary.

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fnothaft commented Jul 20, 2016

I'm going to close this. I think that with recent changes to refactor the RDD package and to privatize code, this effort would now be unnecessary.

@fnothaft fnothaft closed this Jul 20, 2016

@heuermh heuermh modified the milestones: 1.0.0, 0.20.0 Oct 13, 2016

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