[Bioc-devel] scanBam() segfault error

[Martin Morgan]

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 at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>


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