assembly cannot be empty string '""'

[J-Moravec]

In readMeth, the assembly argument cannot be an empty string "".
When saving as DB, this is interpreted as NA and then due to the anyNA checks for header, the header is ignored.

This cause failure of reading the DB due to missing arguments in e.g., new("methylRawDB", ...), which would be otherwise initialized from the header.

methylKit/R/methylDBClasses.R

Lines 279 to 334 in ecf8584

	readMethylRawDB<-function(dbpath,dbtype=NULL,
	sample.id=NULL, assembly=NULL ,context=NULL,
	resolution=NULL,skip=0){
	if(!file.exists(paste0(dbpath,".tbi")))
	{
	Rsamtools::indexTabix(dbpath,seq=1, start=2, end=3,
	skip=skip, comment="#", zeroBased=FALSE)
	}
	# if the tabix file includes a header generated with obj2tabix,
	# it can easily be parsed into the respective object
	head <- checkTabixHeader(tbxFile = dbpath,
	message = paste("No Tabix Header Found,",
	"trying to create methylRawDB from supplied arguments."))
	if(!is.null(head) & !anyNA(head)) {
	if(! any(head$class == c("methylRaw", "methylRawDB") ) ) {
	stop(
	paste("Tabix file does not originate from methylRaw or methylRawDB.\n",
	"Please provide the correct class of data.")
	)
	}
	if(is.null(head$num.records)) {
	num.records=Rsamtools::countTabix(dbpath)[[1]]
	} else num.records = head$num.records
	obj <- new("methylRawDB", dbpath=normalizePath(dbpath),
	num.records=num.records, sample.id = head$sample.ids,
	assembly = head$assembly,context=head$context,
	resolution=head$resolution,dbtype=head$dbtype)
	} else {
	# else we need to generate it from the supplied arguments
	argList <- list(sample.id = sample.id, assembly = assembly,context=context,
	resolution=resolution,dbtype=dbtype)
	checkMissingArg <- sapply(argList,is.null)
	if(any(checkMissingArg)) {
	stop("Missing argument: ",paste(names(argList[checkMissingArg]),collapse = ", "))
	}
	num.records=Rsamtools::countTabix(dbpath)[[1]] ##
	obj <- new("methylRawDB",dbpath=normalizePath(dbpath),num.records=num.records,
	sample.id = sample.id, assembly = assembly,context=context,
	resolution=resolution,dbtype=dbtype)
	}
	if(valid.methylRawDB(obj)) {return(obj)}
	}

Setting a check or at least documenting this behaviour would be IMHO helpful.

[alexg9010]

Thanks for reporting this!
I think it is fair to assume that this argument should not be empty, so we should do a check in methRead already.
Thanks for bringing this to our attention.

Best,
Alex