Hi all,
I ran into a segfault error when trying to read paired-end RNA-seq
alignments with scanBam (see below). This seems to be a problem
introduced in Rsamtools version 1.19.35 (1.19.34 works fine). In case
you need the BAM file for testing, please let me know. Many thanks for
your help.
Leonard
> sessionInfo()
R Under development (unstable) (2014-11-04 r66932)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] Rsamtools_1.19.54 Biostrings_2.35.13 XVector_0.7.4
[4] GenomicRanges_1.19.57 GenomeInfoDb_1.3.20 IRanges_2.1.45
[7] S4Vectors_0.5.23 BiocGenerics_0.13.11
loaded via a namespace (and not attached):
[1] bitops_1.0-6 compiler_3.2.0 tools_3.2.0 zlibbioc_1.13.3
>
> gr <- GRanges("16", IRanges(13173149, 15234449), "+")
>
> file <- BamFile(file, asMates = TRUE)
>
> param <- ScanBamParam(what = scanBamWhat(), which = gr)
>
> tmp <- scanBam(file = file, param = param)
*** caught segfault ***
address 0x14538b1e, cause 'memory not mapped'
Traceback:
1: .Call(func, .extptr(file), space, flag, simpleCigar, tagFilter, ...)
2: doTryCatch(return(expr), name, parentenv, handler)
3: tryCatchOne(expr, names, parentenv, handlers[[1L]])
4: tryCatchList(expr, classes, parentenv, handlers)
5: tryCatch({ .Call(func, .extptr(file), space, flag, simpleCigar,
tagFilter, ...)}, error = function(err) {
stop(conditionMessage(err), "\n f\
ile: ", path(file), "\n index: ", index(file))})
6: .io_bam(.scan_bamfile, file, reverseComplement, yieldSize(file),
tmpl, obeyQname(file), asMates(file), qnamePrefix, qnameSuffix,
param = param)
7: scanBam(file = file, param = param)
8: scanBam(file = file, param = param)
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
