feat: subtract thresholds when calculating QC scores

nextstrain · Jul 15, 2020 · 7f5013b · 7f5013b
1 parent f15af21
commit 7f5013b
Show file tree

Hide file tree

Showing 4 changed files with 5 additions and 5 deletions.
diff --git a/packages/web/src/algorithms/QC/ruleMissingData.ts b/packages/web/src/algorithms/QC/ruleMissingData.ts
@@ -17,7 +17,7 @@ export function ruleMissingData(
 
   let scoreRaw = 0
   if (totalMissing > missingDataThreshold) {
-    scoreRaw = totalMissing * scoreWeight - scoreBias
+    scoreRaw = (totalMissing - missingDataThreshold) * scoreWeight - scoreBias
   }
   const score = clamp(scoreRaw, 0, scoreMax)
 

diff --git a/packages/web/src/algorithms/QC/ruleMixedSites.ts b/packages/web/src/algorithms/QC/ruleMixedSites.ts
@@ -21,7 +21,7 @@ export function ruleMixedSites(
 
   let scoreRaw = 0
   if (totalMixedSites > mixedSitesThreshold) {
-    scoreRaw = totalMixedSites * scoreWeight - scoreBias
+    scoreRaw = (totalMixedSites - mixedSitesThreshold) * scoreWeight - scoreBias
   }
   const score = clamp(scoreRaw, 0, scoreMax)
 

diff --git a/packages/web/src/algorithms/QC/ruleSnpClusters.ts b/packages/web/src/algorithms/QC/ruleSnpClusters.ts
@@ -76,7 +76,7 @@ export function ruleSnpClusters(data: QCInputData, config: QCRulesConfigSNPClust
 
   let scoreRaw = 0
   if (totalSNPs > totalSNPsThreshold) {
-    scoreRaw = totalSNPs * scoreWeight - scoreBias
+    scoreRaw = (totalSNPs - totalSNPsThreshold) * scoreWeight - scoreBias
   }
   const score = clamp(scoreRaw, 0, scoreMax)
 

diff --git a/packages/web/src/algorithms/QC/ruleTotalMutations.ts b/packages/web/src/algorithms/QC/ruleTotalMutations.ts
@@ -17,8 +17,8 @@ export function ruleTotalMutations(
     Object.keys(substitutions).length + Object.keys(insertions).length + Object.keys(deletions).length
 
   let scoreRaw = 0
-  if (totalNumberOfMutations) {
-    scoreRaw = totalNumberOfMutations * scoreWeight - scoreBias
+  if (totalNumberOfMutations > divergenceThreshold) {
+    scoreRaw = (totalNumberOfMutations - divergenceThreshold) * scoreWeight - scoreBias
   }
   const score = clamp(scoreRaw, 0, scoreMax)