R/VcfStack2.R

In gQTLstats: gQTLstats: computationally efficient analysis for eQTL and allied studies

#VcfStack2 <- function(files=NULL, seqinfo=NULL, colData=NULL)
#{
#    if (is.null(files)) {
#        files <- VcfFileList()
#        header <- NULL
#    } else {
#        if (class(files) != "VcfFileList")
#            files = VcfFileList(files)
##        files = indexVcf(files)
#        header <- scanVcfHeader(files[[1]])
#    
#    }   
#
#    if (is.null(seqinfo)) {
#        seqinfo <- if (length(files)) {
#            seqinfo(files)
#        } else Seqinfo()
#    }   
#
#    if (is.null(colData) && length(files)) {
#        colData <- DataFrame(row.names=samples(header))
#    } else {
#        colData <- as(colData, "DataFrame")
#    }   
#
#    if (is.null(rownames(colData)) && length(files))
#         stop("specify rownames in 'colData'")
#
#    new("VcfStack", files=files, colData=colData, seqinfo=seqinfo)
#}