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Support writing RDD[Feature] to various file formats #710

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ryan-williams opened this Issue Jun 4, 2015 · 5 comments

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ryan-williams commented Jun 4, 2015

  • GTF
  • BED
  • .interval_list (cf. #703)
  • NarrowPeak

I'm imagining methods in FeatureRDDFunctions analogous to the {Sam,Bam,Adam,Fastq} methods in AlignmentRecordRDDFunctions.

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laserson Jun 5, 2015

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+1, though this may run into some model incompatibilities.

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laserson commented Jun 5, 2015

+1, though this may run into some model incompatibilities.

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fnothaft Jun 24, 2015

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Do we want this to be automagical or explicit or both?

BTW, I didn't realize you could do subfeatures with the checkboxes. Nifty!

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fnothaft commented Jun 24, 2015

Do we want this to be automagical or explicit or both?

BTW, I didn't realize you could do subfeatures with the checkboxes. Nifty!

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I like the place we netted out at with "reads" files/formats: expose a method that infers format from file format and delegates to other exposed format-specific methods, so that the caller can choose to specify format or not.

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ryan-williams commented Jun 25, 2015

I like the place we netted out at with "reads" files/formats: expose a method that infers format from file format and delegates to other exposed format-specific methods, so that the caller can choose to specify format or not.

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I think that sounds good too. Let's have that be the default approach moving forward.

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fnothaft commented Jun 25, 2015

I think that sounds good too. Let's have that be the default approach moving forward.

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fnothaft Jun 28, 2016

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Closed by 8abb47a.

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fnothaft commented Jun 28, 2016

Closed by 8abb47a.

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