fixing duplicate rname bug for Ensembl GTF parse

thelovelab · Dec 16, 2020 · d48c8d8 · d48c8d8
1 parent 14856f0
commit d48c8d8
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: tximeta
-Version: 1.9.2
+Version: 1.9.3
 Title: Transcript Quantification Import with Automatic Metadata
 Description: Transcript quantification import from Salmon and
     alevin with automatic attachment of transcript ranges and

diff --git a/R/tximeta.R b/R/tximeta.R
@@ -681,9 +681,9 @@ getTxDb <- function(txomeInfo, useHub=TRUE) {
     }
 
     # two cases left:
-    # 1) GENCODE source but AHub didn't work
-    # 2) Neither Ensembl or GENCODE source
-    if (!srcName %in% hubSources || !hubWorked) {
+    # 1) Neither Ensembl or GENCODE source
+    # 2) GENCODE source but AHub didn't work
+    if ((!srcName %in% hubSources) | (srcName == "GENCODE" & !hubWorked)) {
       message("building TxDb with 'GenomicFeatures' package")
       txdb <- makeTxDbFromGFF(txomeInfo$gtf)
       saveDb(