strand in intron counts

intron.saf<-data.frame(GeneID= names(gr.gene)[ol.in],

		       Chr   = seqnames(intron.only),

		       Start = start(intron.only),

                       End	 =   end(intron.only),

                       Strand =  strand(intron.only))

		       End	 =   end(intron.only),stringsAsFactors = F)

exon.saf<-data.frame(GeneID= names(gr.gene)[ol.ex],

		     Chr   = seqnames(unlist(exon)),

		     Start = start(unlist(exon)),

		     End	 =   end(unlist(exon)),

                     Strand =  strand(unlist(exon)))

		     Strand =  strand(unlist(exon)),stringsAsFactors = F)

intron.saf<-dplyr::left_join(intron.saf,unique(exon.saf[,c("GeneID","Strand")]),by=c("GeneID"))

saf <- list(introns=intron.saf,exons=exon.saf)

safout <- paste(out,"/zUMIs_output/expression/",sn,".annotationsSAF.rds",sep="")