Patch to GFF3 reader in rtracklayer

gff-fix.patch

--- a/R/gff.R	2012-03-30 15:59:39.000000000 -0700
+++ b/R/gff.R	2012-05-11 17:36:59.208145562 -0700
@@ -286,13 +286,12 @@
                 lines <- rep(seq_along(attrSplit), elementLengths(attrSplit))
                 attrs <- sub(" *$", "", sub("^ *", "", unlist(attrSplit)))
                 if (is(file, "GFF3File")) {
-                  attrs <- paste(attrs, "=", sep = "")
-                  tvSplit <- strsplit(attrs, "=", fixed=TRUE)
-                  if (any(elementLengths(tvSplit) != 2))
+
+                  equals.pos <- regexpr("=", attrs, fixed=TRUE)
+                  if (any(equals.pos == -1))
                     stop("Some attributes do not conform to 'tag=value' format")
-                  tvMat <- matrix(unlist(tvSplit), nrow = 2)
-                  tags <- tvMat[1,]
-                  vals <- tvMat[2,]
+                  tags <- substr(attrs,1, equals.pos-1)
+                  vals <- substr(attrs,equals.pos+1, nchar(attrs))
                 } else { # split on first space (FIXME: not sensitive to quotes)
                   tags <- sub(" .*", "", attrs) # strip surrounding quotes
                   vals <- sub("^\"([^\"]*)\"$", "\\1",