@@ -199,10 +199,13 @@ setMethod("subseq", "SequenceTrack", function(x, start = NA, end = NA, width = N

 })

 setMethod("subseq", "ReferenceSequenceTrack", function(x, start = NA, end = NA, width = NA) {

+    if (sum(c(is.na(start[1]),is.na(end[1]),is.na(width[1]))) >= 2) {

+      stop("Two out of the three in 'start', 'end' and 'width' have to be provided")

+    }

     if (!is.na(start[1] + end[1] + width[1])) {

         warning("All 'start', 'stop' and 'width' are provided, ignoring 'width'")

         width <- NA

-    }

+    } 

     ## We want start and end to be set if width is provided

     if (!is.na(width[1])) {

         if (is.na(start) && is.na(end)) {

@@ -120,8 +120,8 @@ test_that("subseq works", {

     expect_identical(as.character(subseq(seqTrack.dna, start=1, end=10)), as.character(DNAString("TAAAGGGACT")))

-    expect_error(subseq(SequenceTrack(fastafile, chromosome="chr1")), "at least two out of ")

-    expect_error(subseq(SequenceTrack(fastafile, chromosome="chr1"), start=1), "at least two out of ")

+    expect_error(subseq(SequenceTrack(fastafile, chromosome="chr1")), "Two out of the three in")

+    expect_error(subseq(SequenceTrack(fastafile, chromosome="chr1"), start=1), "Two out of the three in")

     expect_warning(as.character(subseq(SequenceTrack(fastafile, chromosome="chr1"), start=1, end=10, width=10)), "All ")

     expect_error(as.character(subseq(SequenceTrack(fastafile, chromosome="chr1"), start=NA, end=NA, width=10)), "Two ")

     expect_identical(as.character(subseq(SequenceTrack(fastafile, chromosome="chr1"), start=1, width=10)), as.character(DNAString("CTANGAGACG")))

@@ -160,7 +160,7 @@ test_that("conversion of junction to list for plotting works", {

     ## negative filterTolerance

     expect_warning(.convert.summarizedJunctions.to.sashimi.junctions(juns, filter=filt, filterTolerance=-1),

                    "can't be negative, taking absolute value of it")

-    ## transfromation

+    ## transformation

     expect_identical(.convert.summarizedJunctions.to.sashimi.junctions(juns, trans=list(function(x) {x})), out)

     expect_error(.convert.summarizedJunctions.to.sashimi.junctions(juns, trans=1),"must be a function with a single argument")

     expect_error(.convert.summarizedJunctions.to.sashimi.junctions(juns, trans=function(x) {x[-1]}),"invalid output")