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feat: score- and rule-based QC #120

Merged
merged 125 commits into from
Aug 31, 2020
Merged

feat: score- and rule-based QC #120

merged 125 commits into from
Aug 31, 2020

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ivan-aksamentov
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@ivan-aksamentov ivan-aksamentov commented Jul 15, 2020

Resolves: #105 #116

  • have a set of independent QC rules
  • each rule has a set of configuration parameters (e.g. thresholds, coefficients, etc.)
  • each rule outputs a quality score (QC: score-based output #105) as well as optional rule-specific outputs
  • each rule has a specific way to be rendered in the tooltips
  • each rule has a specific way to be rendered in the table
  • each rule has a specific way to be rendered in the export files (using rule-specific outputs)
  • adjust filtering
  • adjust sorting
  • each sequence highlighted with color ranging from pale yellow to bright red, depending on total QC score
  • rules can be configured or disabled independently
  • treat alignment quality and failures as a QC rule, with it's own score (very high weight)
  • normalize score for more precise coloring, filtering and sorting
  • use Nextstrain's tree information to make QC rules even more useful

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QC: score-based output
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