inst/unitTests/test_BamFile.R

In Rsamtools: Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import

fl <- system.file("extdata", "ex1.bam", package="Rsamtools")

test_BamFile_guessIndex <- function()
{
    .BamFile_guessIndex <- Rsamtools:::.BamFile_guessIndex

    bam1 <- tempfile(fileext = ".bam")
    idx1 <- paste0(bam1, ".bai")        # foo.bam.bai
    file.create(idx1)

    bam2 <- tempfile(fileext = ".bam")
    idx2 <- sub(".bam$", ".bai", bam2)  # foo.bai
    file.create(idx2)

    bam3 <- tempfile(fileext = ".bam")  # no index

    fls <- c(bam1, bam2, bam3)

    target <- c(idx1, idx2, NA_character_)
    current <- .BamFile_guessIndex(fls)
    checkIdentical(target, current)

    checkIdentical(character(), .BamFile_guessIndex(character()))
    checkIdentical(character(), .BamFile_guessIndex())
}

test_BamFile_openclose <- function()
{
    .normalizePath <- Rsamtools:::.normalizePath
    bf <- open(BamFile(fl))
    checkTrue(isOpen(bf))
    checkIdentical(.normalizePath(fl), path(bf))
    checkIdentical(sprintf("%s.bai", .normalizePath(fl)), index(bf))
    close(bf)
    checkTrue(!isOpen(bf))
    checkException(close(bf), silent=TRUE)
    bf <- open(bf)                   # open a closed BamFile
    checkTrue(isOpen(bf))
    bf1 <- open(bf)                  # open (clone?) an open BamFile
    checkTrue(isOpen(bf1))
    checkTrue(identical(bf$.extptr, bf1$.extptr))
    ## no extension necessary
    dir.create(fl0 <- tempfile())
    body <- file.path(fl0, "body")
    index <- file.path(fl0, "index")
    file.copy(fl, body)
    file.copy(paste0(fl, ".bai"), index)
    open(bf2 <- BamFile(body, index))
    checkTrue(isOpen(bf2))
}

test_BamFile_isIncomplete <- function()
{
    bf <- BamFile(fl, yieldSize=3000)
    checkIdentical(FALSE, isIncomplete(bf))
    open(bf)
    checkIdentical(TRUE, isIncomplete(bf))
    checkIdentical(3000L, length(scanBam(bf)[[1]][[1]]))
    checkIdentical(TRUE, isIncomplete(bf))
    checkIdentical(307L, length(scanBam(bf)[[1]][[1]]))
    checkIdentical(FALSE, isIncomplete(bf))
    close(bf)
    checkIdentical(FALSE, isIncomplete(bf))
}

test_BamFile_corrupt_index <- function()
{
    fl <- system.file("extdata", "ex1.bam", package="Rsamtools")
    idx <- system.file("unitTests", "cases", "ex1_zero_index.bam.bai")
    bf <- BamFile(fl, idx)
    checkException(suppressWarnings(open(bf)), silent=TRUE)
}

test_BamFile_yield <- function()
{
    bf <- open(BamFile(fl, yieldSize=1000))
    it <- integer()
    while(length(res <- scanBam(bf)[[1]][[1]]))
        it <- append(it, length(res))
    close(bf)
    exp <- c(1000L, 1000L, 1000L, 307L)
    checkIdentical(exp, it)

    bf <- open(BamFile(fl, yieldSize=500))
    which <- GenomicRanges::tileGenome(seqlengths(bf), tilewidth=500,
                                       cut.last.tile.in.chrom=TRUE)
    param <- ScanBamParam(what="rname", which=which)
    it <- integer()
    fun <- function(bf, param) {
        res <- unlist(scanBam(bf, param=param), use.names=FALSE, recursive=FALSE)
        sum(unlist(lapply(res, as.integer)))
    }
    while (res <- fun(bf, param))
        it <- append(it, res)
    close(bf)
    checkIdentical(6L, length(it))
    ## over-count, since reads overlap more than one range
    checkIdentical(5472L, sum(it))
}

test_BamFileList_constructor <- function()
{
    checkTrue(validObject(res <- BamFileList(fl)))
    checkIdentical(fl, path(res[[1]]))
    checkIdentical(sprintf("%s.bai", fl), index(res[[1]]))

    checkTrue(validObject(res <- BamFileList(fl, fl)))
    checkIdentical(fl, path(res[[1]]))
    checkIdentical(fl, index(res[[1]]))
    ## old-style index=character()
    checkTrue(validObject(res <- BamFileList(fl, index=character())))
    checkIdentical(fl, path(res[[1]]))
    checkIdentical(character(0), index(res[[1]], asNA=FALSE))

    ## vector of files
    fl <- c(fl, fl)
    checkTrue(validObject(res <- BamFileList(fl)))
    checkIdentical(fl, unname(path(res)))
    checkIdentical(sprintf("%s.bai", fl), unname(sapply(res, index)))

    checkTrue(validObject(res <- BamFileList(fl, fl)))
    checkIdentical(fl, unname(path(res)))
    checkIdentical(fl, unname(sapply(res, index)))
    ## old-style index=character()
    checkTrue(validObject(res <- BamFileList(fl, index=character())))
    checkIdentical(fl, unname(path(res)))
    checkIdentical(setNames(rep(NA_character_, 2), basename(fl)),
                   index(res))
}

test_BamFileList_yield <- function()
{
    bfl <- unname(BamFileList(c(fl, fl), yieldSize=100))
    checkIdentical(c(100L, 100L), sapply(bfl, yieldSize))

    bfl <- unname(BamFileList(c(fl, fl)))
    checkIdentical(c(NA_integer_, NA_integer_), sapply(bfl, yieldSize))

    ## yieldSize, even implicit on BamFile wins out
    bfl <- BamFileList(BamFile(fl, yieldSize=10), BamFile(fl, yieldSize=20),
                       yieldSize=100)
    checkIdentical(c(10L, 20L), sapply(bfl, yieldSize))

    bfl <- BamFileList(BamFile(fl), BamFile(fl), yieldSize=100)
    checkIdentical(c(NA_integer_, NA_integer_), sapply(bfl, yieldSize))
}

test_BamFile_obeyQname <- function()
{
    srt <- sortBam(fl, tempfile(), byQname=TRUE)
    bf <- BamFile(srt, character(0), yieldSize=1, obeyQname=TRUE)
    scn <- scanBam(bf)
    checkTrue(length(scn[[1]]$qname) == 2)
    checkTrue(length(unique(scn[[1]]$qname)) == 1)

    bf <- BamFile(srt, character(0), yieldSize=2, obeyQname=TRUE)
    scn <- scanBam(bf)
    checkTrue(length(scn[[1]]$qname) == 4)
    checkTrue(length(unique(scn[[1]]$qname)) == 2)

    ## yieldSize is number of unique qnames
    ys <- 1000
    bf <- BamFile(srt, character(0), yieldSize=ys, obeyQname=TRUE)
    scn <- scanBam(bf)
    checkTrue(length(unique(scn[[1]]$qname)) == ys)

    ## yieldSize with 'while'
    bf <- open(BamFile(srt, character(0), yieldSize=500, obeyQname=TRUE))
    it <- integer()
    while (length(res <- scanBam(bf)[[1]]$qname))
        it <- append(it, length(res))
    close(bf)
    checkIdentical(c(974L, 966L, 977L, 390L), it)
}

test_BamFile_asMates_all <- function()
{
    fl <- system.file("extdata", "ex1.bam", package="Rsamtools")
    scn <- scanBam(fl)[[1]]
    scnm <- scanBam(BamFile(fl, asMates=TRUE))[[1]]

    ## qname
    checkTrue(all(scn$qname %in% scnm$qname))
    matenames <- scnm$qname[scnm$mate_status == "mated"]

    ## non-mates off last
    max1 <- max(which(scnm$mate_status == "mated"))
    min0 <- min(which(scnm$mate_status != "mated"))
    checkTrue(max1 < min0)

    ## yieldSize - subset
    flag <- scanBamFlag(isPaired=TRUE,
                        hasUnmappedMate=FALSE,
                        isUnmappedQuery=FALSE)
    param=ScanBamParam(flag=flag, what="qname")
    bf <- BamFile(fl, asMates=FALSE, yieldSize=5)
    bfm <- BamFile(fl, asMates=TRUE, yieldSize=5)
    scn <- scanBam(bf, param=param)[[1]]   ## first 5 records
    scnm <- scanBam(bfm, param=param)[[1]] ## first 5 mates
    checkTrue(length(scn$qname) == 5)
    checkTrue(length(scnm$qname) == 10)

    ## yieldSize - all records
    scnm1 <- scanBam(BamFile(fl, asMates=TRUE))[[1]]
    scnm2 <- scanBam(BamFile(fl, asMates=TRUE, yieldSize=2000))[[1]]
    checkTrue(all(scnm1$qname %in% scnm2$qname))
    checkTrue(all(scnm1$mate_status == scnm2$mate_status))
    checkTrue(all(scnm1$groupid == scnm2$groupid))

    ## yieldSize and which
    bf <- open(BamFile(fl, yieldSize=500))
    which <- GenomicRanges::tileGenome(seqlengths(bf), tilewidth=500,
                                       cut.last.tile.in.chrom=TRUE)
    param <- ScanBamParam(what="rname", which=which)
    it <- integer()
    fun <- function(bf, param) {
        res <- unlist(scanBam(bf, param=param), use.names=FALSE, recursive=FALSE)
        sum(unlist(lapply(res, as.integer)))
    }
    while (res <- fun(bf, param))
        it <- append(it, res)
    close(bf)
    expected <- c(964L, 570L, 1206L, 1418L, 1194L, 120L)
    checkIdentical(expected, it)
}

test_BamFile_asMates_range <- function()
{
    fl <- system.file("extdata", "ex1.bam", package="Rsamtools")
    which <- GRanges("seq1", IRanges(100, width=5))
    param <- ScanBamParam(which=which, what=scanBamWhat())
    scn <- scanBam(fl, param=param)[[1]]
    scnm <- scanBam(BamFile(fl, asMates=TRUE), param=param)[[1]]

    ## qname
    checkTrue(all(scn$qname %in% scnm$qname))
    matenames <- scnm$qname[scnm$mate_status == "mated"]
    checkTrue(length(scnm$qname) == length(scnm$groupid))

    ## non-mates off last
    max1 <- max(which(scnm$mate_status == "mated"))
    min0 <- min(which(scnm$mate_status != "mated"))
    checkTrue(max1 < min0)

    ## range - subset
    flag <- scanBamFlag(isPaired=TRUE,
                        hasUnmappedMate=FALSE,
                        isUnmappedQuery=FALSE)
    param=ScanBamParam(which=which, flag=flag, what=scanBamWhat())
    bf <- BamFile(fl, asMates=FALSE)
    bfm <- BamFile(fl, asMates=TRUE)
    scn <- scanBam(bf, param=param)[[1]]   ## all records in range
    scnm <- scanBam(bfm, param=param)[[1]] ## mates all records in range
    checkTrue(length(scn$qname) == 8)
    checkTrue(length(scnm$qname) == 16)
    checkTrue(sum(scnm$mate_status == "mated") == 16)

    ## range - all records
    which <- GRanges(c("seq1", "seq2"), IRanges(c(0, 0), c(3000, 3000)))
    param <- ScanBamParam(which=which, what=scanBamWhat())
    scnm1 <- scanBam(bfm)[[1]]        ## all records no param
    scnm2<- scanBam(bfm, param=param) ## all records w/ param
    range2A <- scnm2[[1]]
    range2B <- scnm2[[2]]

    len_range <- length(range2A$qname) + length(range2B$qname)
    checkTrue(len_range == length(scnm1$qname))
    mates_range <- sum(range2A$mate_status == "mated",
                       range2B$mate_status == "mated")
    checkTrue(mates_range == sum(scnm1$mate_status == "mated"))
    mates_partition <- length(range2A$.partition) + length(range2B$.partition)
    checkTrue(mates_partition == length(scnm1$.partition))
}

test_BamFile_qname_prefix_suffix <- function()
{
    fl <- system.file("extdata", "ex1.bam", package="Rsamtools")
    checkException(BamFile(fl, qnamePrefixEnd="/:", asMates=TRUE),
                   silent=TRUE)
    checkException(BamFile(fl, qnameSuffixStart="/:", asMates=TRUE),
                   silent=TRUE)

    ## no-op
    target <- c("EAS54_61:4:143:69:578", "EAS54_61:4:143:69:578")
    bfm <- BamFile(fl, asMates=TRUE, qnamePrefixEnd="*")
    scn_noop_1 <- scanBam(bfm, param=ScanBamParam(what="qname"))
    qnames_noop_1 <- scn_noop_1[[1]]$qname[1:2]
    checkIdentical(qnames_noop_1, target)
    bfm <- BamFile(fl, asMates=TRUE, qnameSuffixStart="*")
    scn_noop_2 <- scanBam(bfm, param=ScanBamParam(what="qname"))
    qnames_noop_2 <- scn_noop_2[[1]]$qname[1:2]
    checkIdentical(qnames_noop_2, target)
    qnamePrefixEnd(bfm) <- "*"
    scn_noop_3 <- scanBam(bfm, param=ScanBamParam(what="qname"))
    qnames_noop_3 <- scn_noop_3[[1]]$qname[1:2]
    checkIdentical(qnames_noop_3, target)

    ## setter
    bf <- BamFile(fl, asMates=TRUE)
    checkIdentical(qnamePrefixEnd(bf), NA_character_)
    qnamePrefixEnd(bf) <- "."
    checkIdentical(qnamePrefixEnd(bf), ".")
    qnamePrefixEnd(bf) <- NA_character_;
    checkIdentical(qnamePrefixEnd(bf), NA_character_)

    ## all
    bfm <- BamFile(fl, asMates=TRUE, qnamePrefixEnd="_")
    scn <- scanBam(bfm, param=ScanBamParam(what="qname"))
    qnames <- scn[[1]]$qname[1:2]
    target <- c("61:4:143:69:578", "61:4:143:69:578")
    checkIdentical(qnames, target)

    bfm <- BamFile(fl, asMates=TRUE, qnameSuffixStart=":")
    scn <- scanBam(bfm, param=ScanBamParam(what="qname"))
    qnames <- scn[[1]]$qname[1:2]
    target <- c("EAS54_61:4:143:69", "EAS54_61:4:143:69")
    checkIdentical(qnames, target)

    ## ranges
    bfm <- BamFile(fl, asMates=TRUE)
    which <- GRanges("seq1", IRanges(100, 110))
    param <- ScanBamParam(which=which, what=scanBamWhat())
    target0 <- scanBam(bfm, param=param)[[1]]$qname

    bfm <- BamFile(fl, asMates=TRUE, qnamePrefixEnd="_")
    param <- ScanBamParam(which=which, what="qname")
    qnames <- scanBam(bfm, param=param)[[1]]$qname
    target <- sub(".*_(.*)", "\\1", target0)
    checkTrue(setequal(qnames, target))

    bfm <- BamFile(fl, asMates=TRUE, qnameSuffixStart="_")
    param <- ScanBamParam(which=which, what="qname")
    qnames <- scanBam(bfm, param=param)[[1]]$qname
    target <- sub("(.*)_.*", "\\1", target0)
    checkTrue(setequal(qnames, target))

    bfm <- BamFile(fl, asMates=TRUE, qnameSuffixStart="*")
    param <- ScanBamParam(which=which, what="qname")
    qnames1 <- scanBam(bfm, param=param)[[1]]$qname
    bfm <- BamFile(fl, asMates=TRUE)
    qnames2 <- scanBam(bfm, param=param)[[1]]$qname
    checkIdentical(qnames1, qnames2)
}

test_BamFile_asMates_RNEXT <- function() {
    ## see https://github.com/Bioconductor/Rsamtools/issues/16
    fl <- system.file(package="Rsamtools", "unitTests", "cases", "RNEXT.bam")
    res <- scanBam(BamFile(fl, asMates = TRUE))
    df <- Rsamtools:::.as.data.frame_list_of_lists(res)
    checkIdentical(df$qname, c("r1", "r1", "r2", "r3"))

    ## RNAME == '*' -- don't trust rname, pos (hence strand, qwidth), cigar)
    checkIdentical(df$rname, factor(c("chr4", "chr4", NA, "chr4")))
    checkIdentical(
        df$strand,
        factor(c("+", "-", NA, "-"), levels = c("+", "-", "*"))
    )
    checkIdentical(df$pos, c(100L, 155L, NA, 155L))
    checkIdentical(df$qwidth, c(5L, 5L, NA, 5L))
    checkIdentical(df$mapq, c(99L, 99L, NA, 99L))
    checkIdentical(df$cigar, c("5M", "5M", NA, "5M"))

    ## RNEXT == '*' -- don't trust mrnm, mpos; don't  mate
    checkIdentical(df$mrnm, factor(c("chr4", NA, "chr4", NA)))
    checkIdentical(df$mpos, c(155L, NA, 200L, NA))
    checkIdentical(as.character(df$mate_status), rep("unmated", 4))
}