remove the basename(file) in writeToGTF

suiyue · suiyue · commit d8b975508050 · 2025-01-27T11:39:11.000+08:00
diff --git a/R/readWrite.R b/R/readWrite.R
@@ -232,7 +232,7 @@ writeToGTF <- function(annotation, file, geneIDs = NULL) {
 writeAnnotationsToGTF <- function(annotation, file, geneIDs = NULL, outputExtendedAnno = TRUE, 
                                 outputAll = TRUE, outputBambuModels = TRUE, outputNovelOnly = TRUE){
     if(outputExtendedAnno){
-        writeToGTF(annotation, paste0(basename(file), "extendedAnnotations.gtf"), geneIDs)
+        writeToGTF(annotation, paste0(file, "extendedAnnotations.gtf"), geneIDs)
     }
     if(outputAll){
         annotationAll = setNDR(annotation, 1)

Original file line number	Diff line number	Diff line change
`@@ -232,7 +232,7 @@ writeToGTF <- function(annotation, file, geneIDs = NULL) {`
`232`	`232`	`writeAnnotationsToGTF <- function(annotation, file, geneIDs = NULL, outputExtendedAnno = TRUE,`
`233`	`233`	`outputAll = TRUE, outputBambuModels = TRUE, outputNovelOnly = TRUE){`
`234`	`234`	`if(outputExtendedAnno){`
`235`		`- writeToGTF(annotation, paste0(basename(file), "extendedAnnotations.gtf"), geneIDs)`
	`235`	`+ writeToGTF(annotation, paste0(file, "extendedAnnotations.gtf"), geneIDs)`
`236`	`236`	`}`
`237`	`237`	`if(outputAll){`
`238`	`238`	`annotationAll = setNDR(annotation, 1)`