rtracklayer::import() has no more 'asRangedData' arg

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/cummeRbund@108377 bc3139a8-67e5-0310-9ffc-ced21a209358
gofflab · Sep 10, 2015 · f44df4c · f44df4c
1 parent 9507941
commit f44df4c
Show file tree

Hide file tree

Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: cummeRbund
 Title: Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
-Version: 2.11.1
+Version: 2.11.2
 Date: 2013-04-22
 Author: L. Goff, C. Trapnell, D. Kelley
 Description: Allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data.  In addition, provides numerous plotting functions for commonly used visualizations.

diff --git a/R/database-setup.R b/R/database-setup.R
@@ -1950,7 +1950,7 @@ readCufflinks<-function(dir = getwd(),
 		stop("Must provide a dbConn connection")
 
 	write("Reading GTF file",stderr())
-	gr<-import(gtfFile,asRangedData=FALSE)
+	gr<-import(gtfFile)
 	gr<-as(gr,"data.frame")
 	#gr$genome<-genomebuild
 	colnames(gr)[grepl('^transcript_id$',colnames(gr))]<-'isoform_id'
@@ -1981,7 +1981,7 @@ readCufflinks<-function(dir = getwd(),
 	requiredAttribs <- c("gene_id", "transcript_id", "exon_number")
 
 	if (verbose) message("Importing ", gtfFile)
-	tmp <- import(gtfFile, asRangedData=FALSE)
+	tmp <- import(gtfFile)
 
 	#dispose of unspliced unstranded transcripts
 	#tmp <- tmp[ which(strand(tmp) %in% c('+','-')) ]