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Improvements to speed and memory use

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@ecbush ecbush released this 20 Mar 23:58
v2.0.0
cbad772

This is a major release, meaning things like parameter files and output files have changed.

  • Reduced RAM requirements. We've eliminated the norm score. Synteny scores are now based on raw scores, and thresholds for family formation calculated directly for each strain pair.
  • Improved speed. This results from changes to island formation, and makes a particularly big difference for large data sets (50 or more strains).
  • Simplified the user parameters file. Parameters users are unlikely to ever change have been moved elsewhere.
  • Added plotScoreHists flag. Makes rawSc.pdf, synSc.pdf, coreSynSc.pdf.
  • Introduced several additional classes (LocusFamily, LocusIsland). This is largely for the sake of future development, and should make it easier to capture things like gene duplication.
  • Modified Score class to better organize scores from particular strain pairs. This means the current version of xenoGI will not read scores objects from older versions.
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