... | ... |
@@ -199,10 +199,13 @@ setMethod("subseq", "SequenceTrack", function(x, start = NA, end = NA, width = N |
199 | 199 |
}) |
200 | 200 |
|
201 | 201 |
setMethod("subseq", "ReferenceSequenceTrack", function(x, start = NA, end = NA, width = NA) { |
202 |
+ if (sum(c(is.na(start[1]),is.na(end[1]),is.na(width[1]))) >= 2) { |
|
203 |
+ stop("Two out of the three in 'start', 'end' and 'width' have to be provided") |
|
204 |
+ } |
|
202 | 205 |
if (!is.na(start[1] + end[1] + width[1])) { |
203 | 206 |
warning("All 'start', 'stop' and 'width' are provided, ignoring 'width'") |
204 | 207 |
width <- NA |
205 |
- } |
|
208 |
+ } |
|
206 | 209 |
## We want start and end to be set if width is provided |
207 | 210 |
if (!is.na(width[1])) { |
208 | 211 |
if (is.na(start) && is.na(end)) { |
... | ... |
@@ -120,8 +120,8 @@ test_that("subseq works", { |
120 | 120 |
expect_identical(as.character(subseq(seqTrack.dna, start=1, end=10)), as.character(DNAString("TAAAGGGACT"))) |
121 | 121 |
|
122 | 122 |
|
123 |
- expect_error(subseq(SequenceTrack(fastafile, chromosome="chr1")), "at least two out of ") |
|
124 |
- expect_error(subseq(SequenceTrack(fastafile, chromosome="chr1"), start=1), "at least two out of ") |
|
123 |
+ expect_error(subseq(SequenceTrack(fastafile, chromosome="chr1")), "Two out of the three in") |
|
124 |
+ expect_error(subseq(SequenceTrack(fastafile, chromosome="chr1"), start=1), "Two out of the three in") |
|
125 | 125 |
expect_warning(as.character(subseq(SequenceTrack(fastafile, chromosome="chr1"), start=1, end=10, width=10)), "All ") |
126 | 126 |
expect_error(as.character(subseq(SequenceTrack(fastafile, chromosome="chr1"), start=NA, end=NA, width=10)), "Two ") |
127 | 127 |
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", { |
160 | 160 |
## negative filterTolerance |
161 | 161 |
expect_warning(.convert.summarizedJunctions.to.sashimi.junctions(juns, filter=filt, filterTolerance=-1), |
162 | 162 |
"can't be negative, taking absolute value of it") |
163 |
- ## transfromation |
|
163 |
+ ## transformation |
|
164 | 164 |
expect_identical(.convert.summarizedJunctions.to.sashimi.junctions(juns, trans=list(function(x) {x})), out) |
165 | 165 |
expect_error(.convert.summarizedJunctions.to.sashimi.junctions(juns, trans=1),"must be a function with a single argument") |
166 | 166 |
expect_error(.convert.summarizedJunctions.to.sashimi.junctions(juns, trans=function(x) {x[-1]}),"invalid output") |