test_findSpliceOverlaps-methods.R
In GenomicAlignments: Representation and manipulation of short genomic alignments

## TODO: Add tests for the following "findSpliceOverlaps" methods:
##   findSpliceOverlaps,GAlignments,GRangesList
##   findSpliceOverlaps,GAlignmentPairs,GRangesList
##   findSpliceOverlaps,character,ANY
##   findSpliceOverlaps,BamFile,ANY

.extract <- function(x, col) as.logical(mcols(x)[[col]])

test_findSpliceOverlaps_compatible <- function()
{
    genes <- GRangesList(
        GRanges("chr1", IRanges(5, 15), "+"),
        GRanges("chr1", IRanges(5, 15), "-"))
    reads <- GRangesList(GRanges("chr1", IRanges(3, 13), "+"))
    res <- findSpliceOverlaps(reads, genes[1])
    checkIdentical(FALSE, .extract(res, "compatible"))
    res <- findSpliceOverlaps(reads, genes[2])
    checkIdentical(logical(0), .extract(res, "compatible"))

    ## exact match to intron boundaries
    ## (no overlap between 'reads' and 'genes')
    genes <- GRangesList(
        GRanges("chr1", IRanges(c(5, 20), c(10, 25)), "+"))
    reads <- GRangesList(
        GRanges("chr1", IRanges(11, 19), "+"))
    res <- findSpliceOverlaps(reads, genes)
    checkIdentical(logical(0), .extract(res, "compatible"))

    ## overlap and span intron boundaries
    genes <- GRangesList(
        GRanges("chr1", IRanges(c(5, 20, 30), c(10, 25, 35)), "+"))
    reads <- GRangesList(
        GRanges("chr1", IRanges(5, 12), "+"),
        GRanges("chr1", IRanges(18, 23), "+"),
        GRanges("chr1", IRanges(c(4, 30), c(26, 36)), "+"))
    res <- findSpliceOverlaps(reads[1], genes) ## not a junction read
    checkIdentical(FALSE, .extract(res, "compatible"))
    res <- findSpliceOverlaps(reads[2], genes) ## not a junction read
    checkIdentical(FALSE, .extract(res, "compatible"))
    res <- findSpliceOverlaps(reads[3], genes) ## junction read
    checkIdentical(FALSE, .extract(res, "compatible"))
}

#test_findSpliceOverlaps_novelTSS <- function()
#{
#    ## strand
#    genes <- GRangesList(
#        GRanges("chr1", IRanges(5, 15), "+"),
#        GRanges("chr1", IRanges(5, 15), "-"),
#        GRanges("chr1", IRanges(5, 15), "*"))
#    reads <- GRangesList(GRanges("chr1", IRanges(3, 13), "+"))
#    res <- findSpliceOverlaps(reads, genes[1])
#    checkIdentical(TRUE, .extract(res, "novelTSS"))
#    res <- suppressWarnings(findSpliceOverlaps(reads, genes[2]))
#    checkIdentical(logical(0), .extract(res, "novelTSS"))
#    res <- findSpliceOverlaps(reads, genes[3])
#    checkIdentical(TRUE, .extract(res, "novelTSS"))
#
#    ## multiple matches 
#    genes <- GRangesList(
#        GRanges("chr1", IRanges(15, 20), "+"),
#        GRanges("chr1", IRanges(10, 20), "+"),
#        GRanges("chr1", IRanges(5, 20), "+"))
#    reads <- GRangesList(GRanges("chr1", IRanges(5, 20), "+"))
#    res <- findSpliceOverlaps(reads, genes[1])
#    checkIdentical(TRUE, .extract(res, "novelTSS"))
#    res <- findSpliceOverlaps(reads, genes[1:2])
#    checkIdentical(c(TRUE, TRUE), .extract(res, "novelTSS"))
#    res <- findSpliceOverlaps(reads, genes)
#    checkIdentical(c(FALSE, FALSE, FALSE), .extract(res, "novelTSS"))
#
#    ## junctions
#    genes <- GRangesList(
#        GRanges("chr1", IRanges(c(5, 15), c(10, 20)), "+"))
#    reads <- GRangesList(
#        GRanges("chr1", IRanges(12, 23), "+"),
#        GRanges("chr1", IRanges(3, 18), "+"))
#    res <- findSpliceOverlaps(reads[1], genes)
#    checkIdentical(FALSE, .extract(res, "novelTSS"))
#    res <- findSpliceOverlaps(reads[2], genes)
#    checkIdentical(TRUE, .extract(res, "novelTSS"))
#}
#test_findSpliceOverlaps_novelTSE <- function()
#{
#    ## strand
#    genes <- GRangesList(
#        GRanges("chr1", IRanges(5, 15), "+"),
#        GRanges("chr1", IRanges(5, 15), "-"),
#        GRanges("chr1", IRanges(5, 15), "*"))
#    reads <- GRangesList(GRanges("chr1", IRanges(12, 18), "+"))
#    res <- findSpliceOverlaps(reads, genes[1])
#    checkIdentical(TRUE, .extract(res, "novelTSE"))
#    res <- findSpliceOverlaps(reads, genes[2])
#    checkIdentical(logical(0), .extract(res, "novelTSE"))
#    res <- findSpliceOverlaps(reads, genes[3])
#    checkIdentical(TRUE, .extract(res, "novelTSE"))
#
#    ## multiple matches 
#    genes <- GRangesList(
#        GRanges("chr1", IRanges(5, 15), "+"),
#        GRanges("chr1", IRanges(5, 20), "+"),
#        GRanges("chr1", IRanges(5, 25), "+"))
#    reads <- GRangesList(GRanges("chr1", IRanges(5, 25), "+"))
#    res <- findSpliceOverlaps(reads, genes[1])
#    checkIdentical(TRUE, .extract(res, "novelTSE"))
#    res <- findSpliceOverlaps(reads, genes[1:2])
#    checkIdentical(c(TRUE, TRUE), .extract(res, "novelTSE"))
#    res <- findSpliceOverlaps(reads, genes)
#    checkIdentical(c(FALSE, FALSE, FALSE), .extract(res, "novelTSE"))
#
#    ## junctions
#    genes <- GRangesList(
#        GRanges("chr1", IRanges(c(5, 15), c(10, 20)), "+"))
#    reads <- GRangesList(
#        GRanges("chr1", IRanges(2, 12), "+"),
#        GRanges("chr1", IRanges(18, 23), "+"))
#    res <- findSpliceOverlaps(reads[1], genes)
#    checkIdentical(FALSE, .extract(res, "novelTSE"))
#    res <- findSpliceOverlaps(reads[2], genes)
#    checkIdentical(TRUE, .extract(res, "novelTSE"))
#}
#test_findSpliceOverlaps_novelExon <- function()
#{
#    genes <- GRangesList(
#        GRanges("chr1", IRanges(c(5, 20), c(10, 25)), "+"))
#    ## 'within' intron boundaries
#    reads <- GRangesList(
#        GRanges("chr1", IRanges(c(7, 12, 20), c(10, 18, 23)), "+"))
#    res <- findSpliceOverlaps(reads, genes)
#    checkIdentical(TRUE, .extract(res, "novelExon"))
#
#    ## FIXME :currently TRUE
#    ## Do we want a novel exon to be completely w/in?
#    reads <- GRangesList(
#        GRanges("chr1", IRanges(c(5, 9, 20), c(7, 12, 23)), "+"),
#        GRanges("chr1", IRanges(c(7, 15, 23), c(10, 21, 25)), "+"))
#    res <- findSpliceOverlaps(reads[1], genes)
#    checkIdentical(TRUE, .extract(res, "novelExon"))
#    res <- findSpliceOverlaps(reads[2], genes)
#    checkIdentical(TRUE, .extract(res, "novelExon"))
#
#    ## region not 'intronic' in all transcripts
#    genes <- GRangesList(
#        GRanges("chr1", IRanges(c(5, 20), c(10, 25)), "+"),
#        GRanges("chr1", IRanges(c(5, 20), c(15, 25)), "+"))
#    reads <- GRangesList(
#        GRanges("chr1", IRanges(c(7, 12, 20), c(10, 18, 23)), "+"))
#    res <- findSpliceOverlaps(reads, genes)
#    checkIdentical(c(FALSE, FALSE), .extract(res, "novelExon"))
#}
#test_findSpliceOverlaps_novelRetention <- function()
#{
#    genes <- GRangesList(
#        GRanges("chr1", IRanges(c(5, 20), c(10, 25)), "+"))
#    ## 'within' intron boundaries
#    reads <- GRangesList(
#        GRanges("chr1", IRanges(c(7, 12, 20), c(10, 18, 23)), "+"))
#    res <- findSpliceOverlaps(reads, genes)
#    checkIdentical(TRUE, .extract(res, "novelRetention"))
#
#    ## exact match to intron boundaries
#    ## (no overlap between 'reads' and 'genes')
#    reads <- GRangesList(
#        GRanges("chr1", IRanges(11, 19), "+"))
#    res <- findSpliceOverlaps(reads, genes)
#    checkIdentical(logical(0), .extract(res, "compatible"))
#
#    ## overlap and span intron boundaries
#    genes <- GRangesList(
#        GRanges("chr1", IRanges(c(5, 20, 30), c(10, 25, 35)), "+"))
#    reads <- GRangesList(
#        GRanges("chr1", IRanges(5, 12), "+"), 
#        GRanges("chr1", IRanges(18, 23), "+"),
#        GRanges("chr1", IRanges(c(4, 30), c(26, 36)), "+"))
#    res <- findSpliceOverlaps(reads[1], genes) ## not a junction read
#    checkIdentical(TRUE, .extract(res, "novelRetention"))
#    res <- findSpliceOverlaps(reads[3], genes) ## junction read
#    checkIdentical(TRUE, .extract(res, "novelRetention"))
#
#    ## FIXME : hits a portion of the intronic region
#    ##         but is not completely 'within'
#    ## region is not 'intronic' in all transcripts  
#    genes <- GRangesList(
#        GRanges("chr1", IRanges(c(5, 20), c(10, 25)), "+"),
#        GRanges("chr1", IRanges(c(5, 20), c(15, 25)), "+"))
#    reads <- GRangesList(
#        GRanges("chr1", IRanges(4, 26), "+"))
#    res <- findSpliceOverlaps(reads[1], genes)
#    checkIdentical(c(TRUE, TRUE), .extract(res, "novelRetention"))
#}
#
#test_findSpliceOverlaps_novelSite <- function()
#{
#    genes <- GRangesList(
#        GRanges("chr1", IRanges(c(5, 15), c(10, 20)), "+"))
#    ## single novel site, novel junction
#    reads <- GRangesList(
#        GRanges("chr1", IRanges(c(5, 15), c(7, 20)), "+"))
#    res <- findSpliceOverlaps(reads, genes)
#    checkIdentical(TRUE, .extract(res, "novelSite"))
#    checkIdentical(TRUE, .extract(res, "novelJunction"))
#
#    ## two novel sites, novel junction
#    reads <- GRangesList(
#        GRanges("chr1", IRanges(c(5, 17), c(7, 20)), "+"))
#    res <- findSpliceOverlaps(reads, genes)
#    checkIdentical(TRUE, .extract(res, "novelSite"))
#    checkIdentical(TRUE, .extract(res, "novelJunction"))
#}
#
#test_findSpliceOverlaps_novelJunction <- function()
#{
#    ## novel junction, no novel sites
#    genes <- GRangesList(
#        GRanges("chr1", IRanges(c(5, 20), c(10, 25)), "+"),
#        GRanges("chr1", IRanges(c(5, 22), c(15, 25)), "+"))
#
#    ## query = GRanges 
#    reads <- GRangesList(
#        GRanges("chr1", IRanges(c(5, 20), c(15, 25)), "+"))
#    GRres <- findSpliceOverlaps(reads, genes)
#    checkIdentical(c(TRUE, TRUE), .extract(GRres, "novelJunction"))
#    checkIdentical(c(FALSE, FALSE), .extract(GRres, "novelSite"))
#
#    ## query = GAlignments
#    gal <- GAlignments("chr1", 5L, "11M4N6M", strand("+"))
#    GALres <- findSpliceOverlaps(gal, genes)
#    checkIdentical(c(TRUE, TRUE), .extract(GALres, "novelJunction"))
#    checkIdentical(c(FALSE, FALSE), .extract(GALres, "novelSite"))
#
#    ## query = GAlignmentPairs
#    gal1 <- GAlignments("chr1", 5L, "11M4N6M", strand("+"))
#    gal2 <- GAlignments("chr1", 50L, "6M", strand("-"))
#    galp <- GAlignmentPairs(gal1, gal2)
#    GALPres <- findSpliceOverlaps(galp, genes)
#    checkIdentical(c(TRUE, TRUE), .extract(GALPres, "novelJunction"))
#    checkIdentical(c(FALSE, FALSE), .extract(GALPres, "novelSite"))
#}