169 lines
5.6 KiB
R
169 lines
5.6 KiB
R
###
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test_findOverlaps_IntegerRanges <- function()
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{
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## .....
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## ....
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## ..
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## x
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## xx
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## xxx
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query <- IRanges(c(1, 4, 9), c(5, 7, 10))
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subject <- IRanges(c(2, 2, 10), c(2, 3, 12))
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result <- findOverlaps(query, subject, select = "first")
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checkIdentical(result, c(1L, NA, 3L))
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result <- findOverlaps(query, subject, select = "last")
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checkIdentical(result, c(2L, NA, 3L))
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result <- findOverlaps(query, subject, select = "arbitrary")
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checkIdentical(result, c(2L, NA, 3L))
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checkOverlap <- function(a, q, s, r, c, self=FALSE) {
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target <- Hits(q, s, r, c, sort.by.query=TRUE)
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if (self)
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target <- as(target, "SortedByQuerySelfHits")
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checkIdentical(t(a), t(target))
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}
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result <- findOverlaps(query, subject)
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checkOverlap(result, c(1, 1, 3), c(1, 2, 3), 3, 3)
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## with 'maxgap'
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result <- findOverlaps(query, subject, maxgap = 0L)
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checkOverlap(result, c(1, 1, 2, 3), c(2, 1, 2, 3), 3, 3)
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## with 'minoverlap'
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result <- findOverlaps(query, subject, minoverlap = 3L)
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checkOverlap(result, integer(0), integer(0), 3, 3)
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result <- findOverlaps(query, subject, minoverlap = 2L)
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checkOverlap(result, 1, 2, 3, 3)
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result <- findOverlaps(query, subject, minoverlap = 2L, select = "first")
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checkIdentical(result, c(2L, NA, NA))
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result <- findOverlaps(query, subject, minoverlap = 2L, select = "last")
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checkIdentical(result, c(2L, NA, NA))
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result <- findOverlaps(query, subject, minoverlap = 2L, select = "arbitrary")
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checkIdentical(result, c(2L, NA, NA))
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## zero-width ranges
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query <- IRanges(9:14, 8:13)
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result <- findOverlaps(query, subject, minoverlap = 1L)
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checkOverlap(result, integer(0), integer(0), 6, 3)
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result <- findOverlaps(query, subject)
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checkOverlap(result, c(3, 4), c(3, 3), 6, 3)
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result <- findOverlaps(query, subject, maxgap = 0L)
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checkOverlap(result, 2:5, c(3, 3, 3, 3), 6, 3)
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result <- findOverlaps(query, subject, maxgap = 1L)
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checkOverlap(result, 1:6, c(3, 3, 3, 3, 3, 3), 6, 3)
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result <- findOverlaps(subject, query, minoverlap = 1L)
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checkOverlap(result, integer(0), integer(0), 3, 6)
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result <- findOverlaps(subject, query)
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checkOverlap(result, c(3, 3), c(3, 4), 3, 6)
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result <- findOverlaps(subject, query, maxgap = 0L)
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checkOverlap(result, c(3, 3, 3, 3), 2:5, 3, 6)
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result <- findOverlaps(subject, query, maxgap = 1L)
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checkOverlap(result, c(3, 3, 3, 3, 3, 3), 1:6, 3, 6)
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## .....
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## ....
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## ..
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## xxxx
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## xxx
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query <- IRanges(c(1, 4, 9), c(5, 7, 10))
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subject <- IRanges(c(2, 2), c(5, 4))
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result <- findOverlaps(query, subject)
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checkOverlap(result, c(1, 1, 2, 2), c(1, 2, 1, 2), 3, 2)
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result <- findOverlaps(subject, query)
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checkOverlap(result, c(1, 1, 2, 2), c(1, 2, 1, 2), 2, 3)
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query <- IRanges(c(1, 4, 9, 11), c(5, 7, 10, 11))
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result <- findOverlaps(query)
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checkOverlap(result, c(1, 1, 2, 2, 3, 4), c(1, 2, 1, 2, 3, 4), 4, 4, TRUE)
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## check case of identical subjects
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## .....
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## .....
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## ..
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## xxxx
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## xxxx
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## xx
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## xxx
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## xx
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query <- IRanges(c(1, 4, 9), c(5, 7, 10))
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subject <- IRanges(c(2, 2, 6, 6, 6), c(5, 5, 7, 8, 7))
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result <- findOverlaps(query, subject)
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checkOverlap(result, c(1, 1, 2, 2, 2, 2, 2), c(1, 2, 1, 2, 3, 4, 5), 3, 5)
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subject <- IRanges(c(1, 6, 13), c(4, 9, 14)) # single points
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checkIdentical(findOverlaps(c(3L, 7L, 10L), subject, select = "first"),
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c(1L, 2L, NA))
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checkIdentical(findOverlaps(c(3L, 7L, 10L), subject, select = "last"),
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c(1L, 2L, NA))
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checkIdentical(findOverlaps(c(3L, 7L, 10L), subject, select = "arbitrary"),
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c(1L, 2L, NA))
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checkIdentical(findOverlaps(IRanges(c(2,1),c(3,4)), subject),
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Hits(1:2, c(1, 1), 2, 3, sort.by.query=TRUE))
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## check other types of matching
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## ..
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## ..
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## ....
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## ......
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## xxxx
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## xxxx
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## xxxxx
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## xxxx
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query <- IRanges(c(1, 5, 3, 4), width=c(2, 2, 4, 6))
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subject <- IRanges(c(1, 3, 5, 6), width=c(4, 4, 5, 4))
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## 'start'
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result <- findOverlaps(query, subject, type = "start")
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checkOverlap(result, c(1, 2, 3), c(1, 3, 2), 4, 4)
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## minoverlap > 1L
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result <- findOverlaps(query, subject, type = "start", minoverlap = 3L)
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checkOverlap(result, 3, 2, 4, 4)
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## 'end'
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result <- findOverlaps(query, subject, type = "end")
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checkOverlap(result, c(2, 3, 4, 4), c(2, 2, 3, 4), 4, 4)
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result <- findOverlaps(subject, query, type = "end")
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checkOverlap(result, c(2, 2, 3, 4), c(2, 3, 4, 4), 4, 4)
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## select = "first"
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result <- findOverlaps(query, subject, type = "end", select = "first")
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checkIdentical(result, c(NA, 2L, 2L, 3L))
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## 'within'
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result <- findOverlaps(query, subject, type = "within")
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checkOverlap(result, c(1, 2, 2, 3), c(1, 2, 3, 2), 4, 4)
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## 'equal'
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result <- findOverlaps(query, subject, type = "equal")
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checkOverlap(result, 3, 2, 4, 4)
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checkException(findOverlaps(query, NULL), silent = TRUE)
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checkException(findOverlaps(NULL, query), silent = TRUE)
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}
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test_subsetByOverlaps_IntegerRanges <- function() {
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x <- IRanges(9:12, 15)
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ranges <- IRanges(1, 10)
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checkIdentical(x[1:2], subsetByOverlaps(x, ranges))
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checkIdentical(x[3:4], subsetByOverlaps(x, ranges, invert=TRUE))
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checkIdentical(x[1:3], subsetByOverlaps(x, ranges, maxgap=0))
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checkIdentical(x[4], subsetByOverlaps(x, ranges, maxgap=0, invert=TRUE))
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x <- IRanges(c(1, 4, 9), c(5, 7, 10))
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ranges <- IRanges(c(6, 8, 10), c(7, 12, 14))
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checkIdentical(x[2:3], subsetByOverlaps(x, ranges))
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checkIdentical(x[1], subsetByOverlaps(x, ranges, invert=TRUE))
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checkIdentical(x, subsetByOverlaps(x, ranges, maxgap=0))
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checkIdentical(x[0], subsetByOverlaps(x, ranges, maxgap=0, invert=TRUE))
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}
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