fix: adjust NDR threshold behavior. Previously, NDR = 1 would override remove.subset and min.sampleNumber. Now, NDR = 0.999 and NDR = 1 produce identical results except for the NDR threshold itself.

SuiYue-2308 · SuiYue-2308 · commit 25aa6794805f · 2026-04-15T14:06:53.000+08:00
diff --git a/R/bambu-extendAnnotations-utilityExtend.R b/R/bambu-extendAnnotations-utilityExtend.R
@@ -112,7 +112,7 @@ filterTranscriptsByAnnotation <- function(rowDataCombined, annotationGrangesList
   } else if(is.null(NDR)) {
           NDR <- 0.5
   }
-  filterSet <- (rowDataCombined$NDR <= NDR | rowDataCombined$readClassType == "equal:compatible")
+  filterSet <- ((!is.na(rowDataCombined$NDR) & rowDataCombined$NDR <= NDR) | rowDataCombined$readClassType == "equal:compatible")
   lowConfidenceTranscripts <- combindRowDataWithRanges(
         rowDataCombined[!filterSet,], 
         exonRangesCombined[!filterSet])
@@ -224,7 +224,7 @@ calculateNDROnTranscripts <- function(combinedTranscripts, useTxScore = FALSE){
     } else {
         combinedTranscripts$NDR <- calculateNDR(combinedTranscripts$maxTxScore, equal)
     }
-    combinedTranscripts$NDR[combinedTranscripts$maxTxScore==-1] <- 1
+    combinedTranscripts$NDR[combinedTranscripts$maxTxScore==-1] <- NA
     return(combinedTranscripts)
 }
 

Original file line number	Diff line number	Diff line change
`@@ -112,7 +112,7 @@ filterTranscriptsByAnnotation <- function(rowDataCombined, annotationGrangesList`
`112`	`112`	`} else if(is.null(NDR)) {`
`113`	`113`	`NDR <- 0.5`
`114`	`114`	`}`
`115`		`- filterSet <- (rowDataCombined$NDR <= NDR \| rowDataCombined$readClassType == "equal:compatible")`
	`115`	`+ filterSet <- ((!is.na(rowDataCombined$NDR) & rowDataCombined$NDR <= NDR) \| rowDataCombined$readClassType == "equal:compatible")`
`116`	`116`	`lowConfidenceTranscripts <- combindRowDataWithRanges(`
`117`	`117`	`rowDataCombined[!filterSet,],`
`118`	`118`	`exonRangesCombined[!filterSet])`
`@@ -224,7 +224,7 @@ calculateNDROnTranscripts <- function(combinedTranscripts, useTxScore = FALSE){`
`224`	`224`	`} else {`
`225`	`225`	`combinedTranscripts$NDR <- calculateNDR(combinedTranscripts$maxTxScore, equal)`
`226`	`226`	`}`
`227`		`- combinedTranscripts$NDR[combinedTranscripts$maxTxScore==-1] <- 1`
	`227`	`+ combinedTranscripts$NDR[combinedTranscripts$maxTxScore==-1] <- NA`
`228`	`228`	`return(combinedTranscripts)`
`229`	`229`	`}`
`230`	`230`