From 7f5013b54069f91f63edd76174ee08be4c15ebef Mon Sep 17 00:00:00 2001
From: ivan-aksamentov <ivan.aksamentov@gmail.com>
Date: Wed, 15 Jul 2020 10:22:15 +0200
Subject: [PATCH] feat: subtract thresholds when calculating QC scores

---
 packages/web/src/algorithms/QC/ruleMissingData.ts    | 2 +-
 packages/web/src/algorithms/QC/ruleMixedSites.ts     | 2 +-
 packages/web/src/algorithms/QC/ruleSnpClusters.ts    | 2 +-
 packages/web/src/algorithms/QC/ruleTotalMutations.ts | 4 ++--
 4 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/packages/web/src/algorithms/QC/ruleMissingData.ts b/packages/web/src/algorithms/QC/ruleMissingData.ts
index 1d8e54c66..10badd190 100644
--- 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
index f70a29d86..61aec71c9 100644
--- 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
index d935173c2..479a05ab8 100644
--- 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
index 860415953..6c97b5f72 100644
--- 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)