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broadinstitute / gatk

Official code repository for GATK versions 4 and up
https://software.broadinstitute.org/gatk
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Performance issues when accessing Reads in Interval/Feature based walkers. #1246

Open vruano opened 8 years ago

vruano commented 8 years ago

I currently have a feature driven walker in gatk-protected that is slower than a read-walker equivalent due to the repetitive Read iterator re-instantiation when accessing overlapping reads using the ReadContext.

Ideally the engine (FeatureManager?) would try to reuse open read iterators instead of creating them for each feature/interval.

droazen commented 8 years ago

We will definitely do this for beta!

droazen commented 8 years ago

Since this was specifically requested by @vruano, we should attempt it for alpha-1.