### R code from vignette source 'vignettes/GenomicRanges/inst/doc/countGenomicOverlaps.Rnw'

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### code chunk number 1: firstExample (eval = FALSE)
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## library(TxDb.Hsapiens.UCSC.hg18.knownGene)
## txdb <- Hsapiens_UCSC_hg18_knownGene_TxDb
## ranges <- exonsBy(txdb, "tx")
## bamFiles <- c("sample1.bam", "sample2.bam")
## 
## countsTable <-
##     as.data.frame(tx_id=rep(names(ranges), elementLengths(ranges)),
##         exon_id=values(unlist(ranges))[["exon_id"]],
##         sapply(bamFiles, function(bamFile, ranges) {
##             aln <- readGappedAlignments(bamFile)
##             countGenomicOverlaps(ranges, aln)
##         }, ranges))


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### code chunk number 2: data
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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="+")

query <- 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))

subj <- 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))


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### code chunk number 3: typeAny
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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 = none,
               divide = divide,
               uniqueDisjoint = uniqueDisjoint)
rownames(res_any) <- paste("F", seq_len(16), sep="")
res_any


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### code chunk number 4: typeWithin
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none <- countGenomicOverlaps(query, subj, type="within", resolution="none")
divide <- countGenomicOverlaps(query, subj, type="within", resolution="divide")
res_within <- data.frame(none = none,
                         divide = divide)
rownames(res_within) <- paste("F", seq_len(16), sep="")
res_within