Reading VCF file features using custom 'Allele' subclass

[makenzi-nzau]

Hi!

I'm writing an application using HTSJDK 3.0.4 to read the contents of a VCF file.
The application traverses AbstractFeatureReader<VariantContext,LineIterator> with
a CloseableTribbleIterator<VariantContext> .
I would like the VariantContexts of this iterator to use a custom subclass of Allele instead of the default SimpleAllele.
This would also include the Genotype objects contained within.
What would be the idiomatic way to do this in the current API?

Thank you for your time,

Makenzi Nzau.

[lbergelson]

@makenzi-nzau That's a great question. Unfortunately I don't have a great answer. The simple answer is that there's no easy way to make the AbstractFeatureReader provide an iterator that does what you want.

I think the simplest thing to do, but it might not be what you want, is to wrap the produced iterator in a new iterator that internally repackages the produced VariantContexts with your Allele implementation.

A more involved procedure would be to implement your own subclass of AbstractFeatureReader which does what you want and then explicitly invoke that.

Neither is really is likely to be a great option unfortunately. I think WHY you want a new implementation of Allele and what you want to do with it is an important question which informs which way you have to go to achieve it.

I've wanted for a long time to make VariantContext/Genotype also interfaces with more facilities to actually swap out implementations to be what you need, but it's never been prioritized.

[makenzi-nzau]

Thank you!
This clarifies the design space of my application considerably;