search

samtools / htsjdk

A Java API for high-throughput sequencing data (HTS) formats.
http://samtools.github.io/htsjdk/
277 stars 244 forks source link

GenotypeLikelihoods should handle anyploid, not just diploid #437

Closed ronlevine closed 8 years ago

ronlevine commented 8 years ago

GenotypeLikelihoodsAllelePair GenotypeLikelihoods.getAllelePair(final int PLindex) returns the cached alleles corresponding to the PLindex. This cache is diploid because the method that initializes it, GenotypeLikelihoodsAllelePair[] GenotypeLikelihoods.calculatePLcache(final int altAlleles), uses a diploid number of likelihoods ( numLikelihoods(1 + altAlleles, 2)) and adds an allele pair each PLindex, instead of the ploidy number of allele indices. If the methods are generalized, they should return ArrayList<Integer> instead of GenotypeLikelihoodsAllelePair.

yfarjoun commented 8 years ago

hmmm. I think that the optimization of using a GenotypeLikelihoodsAllelePair overweighs the generalizability of multipliody.

is there a usecase for this?

yfarjoun commented 8 years ago

is it needed for select variants? perhaps a non-diploid method could be added rather than changing the signature of this function.

ronlevine commented 8 years ago

Here's the usecase: https://github.com/broadinstitute/gatk/issues/1382 The plan is to keep the diploid optimization. Combinatorials with binomials is very compute intensive.

ronlevine commented 8 years ago

@yfarjoun Could you review the accompanying pull request? It should be ready momentarily.

yfarjoun commented 8 years ago

It will not be this week, as I"m out conferencing in agbt. but if it can wait for next week then sure.

Y.

On Tue, Feb 9, 2016 at 9:40 AM, Ron Levine notifications@github.com wrote:

@yfarjoun https://github.com/yfarjoun Could you review the accompanying pull request? It should be ready momentarily.

— Reply to this email directly or view it on GitHub https://github.com/samtools/htsjdk/issues/437#issuecomment-181895468.

ronlevine commented 8 years ago

@yfarjoun Thanks. I'll look at your comments next week while I'm in Miami.

ronlevine commented 8 years ago

I think this should be closed.