Thanks Martin. I had one other test case that resulted in a segfault.
I just tried Rsamtools 1.21.1 and both cases work fine with the new
version. Thanks for your help and for fixing this so quickly.
Leonard
On Mon, Apr 20, 2015 at 10:59 AM, Martin Morgan <mtmor...@fredhutch.org> wrote:
> On 04/17/2015 09:12 AM, Martin Morgan wrote:
>>
>> On 04/17/2015 08:59 AM, Leonard Goldstein wrote:
>>>
>>> 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
>>
>>
>> Probably a BAM file would be a big help... Thanks, Martin
>
>
> Thanks Leonard, I think this is addressed in 1.20.1 / 1.21.1, which are not
> yet available via biocLite.
>
> I will likely revisit this code in the next week or so; please let me know
> if there are other issues.
>
>
> Martin
>
>>
>>> 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
>>>
>>
>>
>
>
> --
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793
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