Merge pull request #451 from GoekeLab/fix_denovo_bug

andredsim · web-flow · commit 1e097994045b · 2024-10-25T14:04:28.000+08:00
Fix typo in extendAnnotations
diff --git a/R/bambu-extendAnnotations-utilityExtend.R b/R/bambu-extendAnnotations-utilityExtend.R
@@ -108,7 +108,7 @@ filterTranscriptsByAnnotation <- function(rowDataCombined, annotationGrangesList
     exonRangesCombined <- exonRangesCombined[filterSet]
     rowDataCombined <- rowDataCombined[filterSet,]
   }
-  if(sum(filterSet==0) & length(annotationGrangesList)==0) stop(
+  if(sum(filterSet)==0 & length(annotationGrangesList)==0) stop(
     "WARNING - No annotations were provided. Please increase NDR threshold to use novel transcripts")
   if(sum(filterSet)==0) message("WARNING - No novel transcripts meet the given thresholds. Try a higher NDR.")
   # (3) combine novel transcripts with annotations

Original file line number	Diff line number	Diff line change
`@@ -108,7 +108,7 @@ filterTranscriptsByAnnotation <- function(rowDataCombined, annotationGrangesList`
`108`	`108`	`exonRangesCombined <- exonRangesCombined[filterSet]`
`109`	`109`	`rowDataCombined <- rowDataCombined[filterSet,]`
`110`	`110`	`}`
`111`		`- if(sum(filterSet==0) & length(annotationGrangesList)==0) stop(`
	`111`	`+ if(sum(filterSet)==0 & length(annotationGrangesList)==0) stop(`
`112`	`112`	`"WARNING - No annotations were provided. Please increase NDR threshold to use novel transcripts")`
`113`	`113`	`if(sum(filterSet)==0) message("WARNING - No novel transcripts meet the given thresholds. Try a higher NDR.")`
`114`	`114`	`# (3) combine novel transcripts with annotations`