diff --git a/DESCRIPTION b/DESCRIPTION index 878ecbe..210935e 100644 --- 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 index 8e993e2..c150d39 100644 --- 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('+','-')) ]