###################################################
### chunk number 1: data
###################################################
#line 50 "vignettes/GenomicRanges/inst/doc/countGenomicOverlaps.Rnw"
library(GenomicFeatures)

rng1 <- function(s, w)
GRanges(seq="chr1", IRanges(s, width=w), strand="+")
rng2 <- function(s, w)
GRanges(seq="chr2", IRanges(s, width=w), strand="+")

subj <- GRangesList(G1=rng1(1000, 500),
                    G2=rng2(2000, 900),
                    G3=rng1(c(3000, 3600), c(500, 300)),
                    G4=rng2(c(7000, 7500), c(600, 300)),
                    G5=rng2(c(9000, 9000), c(300, 600)),
                    G6=rng1(4000, 500),
                    G7=rng1(c(4300, 4500), c(400, 400)),
                    G8=rng2(3000, 500),
                    G9=rng1(c(5000, 5600), c(500, 300)),
                    G10=rng1(6000, 500),
                    G11=rng1(6600, 400))

query <- GRangesList(read1=rng1(1400, 500),
                     read2=rng2(2700, 100),
                     read3=rng1(3400, 300),
                     read4=rng2(7100, 600),
                     read5=rng2(9000, 200),
                     read6=rng1(4200, 500),
                     read7=rng2(c(3100, 3300), 50),
                     read8=rng1(c(5400, 5600), 50),
                     read9=rng1(c(6400, 6600), 50))


###################################################
### chunk number 2: typeAny
###################################################
#line 242 "vignettes/GenomicRanges/inst/doc/countGenomicOverlaps.Rnw"
none <- countGenomicOverlaps(query, subj, type="any",
                                  resolution="none")
divide <- countGenomicOverlaps(query, subj, type="any",
                               resolution="divide")
uniqueDisjoint <- countGenomicOverlaps(query, subj, type="any",
                                       resolution="uniqueDisjoint")

res_any <- data.frame(
               none = values(unlist(none))[["hits"]],
               divide = round(values(unlist(divide))[["hits"]], 2),
               uniqueDisjoint = values(unlist(uniqueDisjoint))[["hits"]])
rownames(res_any) <- paste("F", seq_len(16), sep="")
res_any


###################################################
### chunk number 3: typeWithin
###################################################
#line 270 "vignettes/GenomicRanges/inst/doc/countGenomicOverlaps.Rnw"
none <- countGenomicOverlaps(query, subj, type="within", resolution="none")
divide <- countGenomicOverlaps(query, subj, type="within", resolution="divide")
res_within <- data.frame(none = values(unlist(none))[["hits"]],
                         divide = values(unlist(divide))[["hits"]])
rownames(res_within) <- paste("F", seq_len(16), sep="")
res_within