minimize requests when 2bit files have many sequences

dasmoth / dalliance

Interactive web-based genome browser.

http://www.biodalliance.org/

BSD 2-Clause "Simplified" License

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minimize requests when 2bit files have many sequences #165

Closed ajo2995 closed 9 years ago

ajo2995 commented 9 years ago

I ended up creating an EnsemblSequenceSource instead of using TwoBit sources because we have some assemblies that are extremely fragmented (~500,000 scaffolds) which were taking too long to initialize

dasmoth commented 9 years ago

Thanks very much for this. I guess the .2bit format isn't really optimised for the million-contigs case, but your optimisations are welcome anyway.

EnsemblSequenceSource is also good to have. I may do a slight refactoring here before the 0.14 release, because we're trying to move away from having a proliferation of per-source-type "ensemblURI" type parameters.