fixed processing of missing genotype option in backend regression code

stjude · Nov 7, 2023 · 78f0d5a · 78f0d5a
1 parent ed56ade
commit 78f0d5a
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Showing 2 changed files with 2 additions and 6 deletions.
diff --git a/client/termsetting/handlers/snplst.ts b/client/termsetting/handlers/snplst.ts
@@ -554,7 +554,7 @@ function validateQ(data: any) {
 	if (data.q.AFcutoff < 0 || data.q.AFcutoff > 100) throw 'AFcutoff is not within 0 to 100'
 	if (![0, 1, 2].includes(data.q.alleleType)) throw 'alleleType value is not one of 0/1'
 	if (![0, 1, 2, 3].includes(data.q.geneticModel)) throw 'geneticModel value is not one of 0/1'
-	if (![0, 1, 2].includes(data.q.missingGenotype)) throw 'missingGenotype value is not one of 0/1'
+	if (![0, 1].includes(data.q.missingGenotype)) throw 'missingGenotype value is not one of 0/1'
 }
 
 export async function fillTW(tw: SnpsTermWrapper, vocabApi: SnpsVocabApi) {

diff --git a/server/src/termdb.regression.js b/server/src/termdb.regression.js
@@ -1276,7 +1276,7 @@ tw{}
 		cacheid
 		alleleType: 0/1
 		geneticModel: 0/1/2/3
-		missingGenotype: 0/1/2
+		missingGenotype: 0/1
 		snp2effAle{}
 		snp2refGrp{}
 samples {Map}
@@ -1459,10 +1459,6 @@ function doImputation(snp2sample, tw, cachesampleheader, sampleinfilter) {
 		return
 	}
 	if (tw.q.missingGenotype == 1) {
-		// numerically as average value
-		throw 'not done'
-	}
-	if (tw.q.missingGenotype == 2) {
 		// drop sample
 		const incompleteSamples = new Set() // any samples with missing gt
 		for (const { samples } of snp2sample.values()) {