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v2.2.0

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@TimD1 TimD1 released this 25 Oct 14:47
· 124 commits to master since this release

Improved phase set/block analysis

  • vcfdist now skips unphased variants by default
  • add phasing info from PS tag
  • switch "errors" only counted if they occur within phase sets
  • added phase set count and NG50 (inputs)
  • calculated phase block NG50 (break on switches) and NGC50 (break on flips and switches)
  • reorganization and variable renaming in phase.cpp

General improvements

  • VCF parsing and warnings are more concise/consistent
  • allow variant selection by FILTER
  • truth and query variants are no longer realigned by default
  • removed unnecessary data copying from sort_superclusters() which significantly improves overall runtime and fixes uncounted runtime