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  • BundleData::refseq and BundleData::gseq should be bundled together as a shared pointer to a reference seq data structure (e.g. similar to GRefData) , reference counted , as in a multi-threaded environment there could be many/multiple bundles sharing that info and it is wasteful to duplicate it for every bundle

  • we should get rid of that terrible hashing hack (appending a dummy suffix, id+=) in rlink.cpp processRead(), by using a better hash function

  • implement a better SPMC threading model with less locking -- perhaps one with a queue per consumer/worker? However, multiple small bundles should be packaged together (say 100 tiny bundles at once) and passed on to a worker thread all at once.