[Bioc-devel] Rsamtools: applyPileups seg fault (!!)

[Dan Gatti]

I'm trying to pileup some BAMs and I'm finding that certain loci in certain files produce seg faults. I've tried to find some common property, but I'm at a loss. I've selected a single locus in a single file that reproducibly produces the problem.  The BAM file and its index are on our FTP site. Here is the script and its output:

library(Rsamtools)

file = "ftp://ftp.jax.org.dgatti/M143.final.sorted.bam"
pf = PileupFiles(file)
pileupfxn = function(x) {
    x$seq
} # pileupfxn
gr = GRanges(seqnames = "chr11",
     ranges = IRanges(start = c(58109576, 58111391), width = c(1,1)))
puparam = PileupParam(minBaseQuality = 20L, what = "seq", which = gr)
pu = applyPileups(files = pf, FUN = pileupfxn, param = puparam)

*** caught segfault ***
address 0xffffffffce138f6c, cause 'memory not mapped'

Traceback:
1: .Call(.apply_pileups, extptr, names(files), space, param, FUN)
2: doTryCatch(return(expr), name, parentenv, handler)
3: tryCatchOne(expr, names, parentenv, handlers[[1L]])
4: tryCatchList(expr, classes, parentenv, handlers)
5: tryCatch({    param <- as(param, "list")    extptr <- lapply(files, .extptr)    space <- if (0L != length(param[["which"]]))         .asSpace(param[["which"]])    else NULL    param[["what"]] <- c("seq", "qual") %in% param[["what"]]    .Call(.apply_pileups, extptr, names(files), space, param,         FUN)}, error = function(err) {    stop("applyPileups: ", conditionMessage(err), call. = FALSE)})
6: applyPileups(files = pf, FUN = pileupfxn, param = puparam)
7: applyPileups(files = pf, FUN = pileupfxn, param = puparam)

And here is the sessionInfo().  I can reproduce this on Windows and Linux. I haven't tested on a Mac.

> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] LC_CTYPE=en_US       LC_NUMERIC=C         LC_TIME=en_US
[4] LC_COLLATE=en_US     LC_MONETARY=en_US    LC_MESSAGES=en_US
[7] LC_PAPER=en_US       LC_NAME=C            LC_ADDRESS=C
[10] LC_TELEPHONE=C       LC_MEASUREMENT=en_US LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] Rsamtools_1.16.1     Biostrings_2.32.1    XVector_0.4.0
[4] GenomicRanges_1.16.4 GenomeInfoDb_1.0.2   IRanges_1.22.10
[7] BiocGenerics_0.10.0

loaded via a namespace (and not attached):
[1] bitops_1.0-6    stats4_3.1.0    zlibbioc_1.10.0

Any help or thoughts would be appreciated.

Thanks,
Dan

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