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Bioconductor / VariantAnnotation

Annotation of Genetic Variants
https://bioconductor.org/packages/VariantAnnotation
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moved vcfFields() from 'SimpleList()' into 'CharacterList()' #12

Closed Liubuntu closed 6 years ago

Liubuntu commented 6 years ago

Hi @vobencha ,

This new pull request has changed the returned value from vcfFields() into a SimpleCharacterList. Please take a look. Thanks!

Best, Qian

vobencha commented 6 years ago

I didn't realize the default behavior of CharacterList() was to create a CompressedCharacterList (not SimpleCharacterList). I don't have a preference, I was just trying to go with what I thought the default would be.

I'm fine with the CompressedCharacterList and think we should leave the door open for the other derivative, SimpleCharacterList. In the interest of being as generic as possible, please change these things:

Thanks.

Liubuntu commented 6 years ago

Hi @vobencha ,

Now everything is in generic CharacterList(), with the default compress=TRUE. The link of IRanges is also added into the documentation. Thanks!

Best, Qian

Liubuntu commented 6 years ago

Thanks Val! The pull request for GenomicFiles is also ready. It depends on the VariantAnnotation 1.27.6 now, and has the \link[IRanges]{CharacterList} in the documentation also. Can you take a quick look at this one also? Thanks! https://github.com/Bioconductor/GenomicFiles/pull/1/commits/a03971eb89c9deafccc20786bed386df8af2aa25

mtmorgan commented 6 years ago

I'll look at GenomicFiles.