[BioC] 'Rsamtools' produces segfaults with XS tag

[Martin Morgan]

  On 8/13/2010 2:11 PM, Misha Kapushesky wrote:
> Hi,
>
> I put it on 
> http://www.ebi.ac.uk/~ostolop/accepted_hits.sortednames.bam. After 
> some more tinkering - it seems I can't reproduce this on my Mac, only 
> on our Linux install. I also just noticed that the released version is 
> 1.0.7, while we seem to have 1.1.11, and yet our R is 2.11.1 - perhaps 
> it's a version incompatibility and we managed to install ourselves 
> something incompatible? If that's the case, we'll probably try to get 
> a more standard install going, and hopefully the problem will go away...
>

This should be fixed in 1.0.8 (release) or 1.1.12 (devel), available via 
biocLite in the next several days or via svn 
(http://bioconductor.org/developers/source-control/) immediately.

Thanks for the report and sample data.

Martin

> --Misha
>
> On Fri, 13 Aug 2010, Martin Morgan wrote:
>
>> Thanks Misha for the additional hints; I looked at the code and couldn't
>> see anything immediately wrong, but if you can provide a (minimal?)  bam
>> file displaying the problem that would be helpful. Martin
>>
>> Misha Kapushesky <ostolop at ebi.ac.uk> writes:
>>
>>> Hi,
>>>
>>> I can add more detail to this - the same problem:
>>>
>>>> library( "Rsamtools" )
>>> ...
>>>> tags <- c("NM", "MD", "XA", "XS","NS")
>>>> and_file = "SRR034792/tophat_out/accepted_hits.sortednames.bam"
>>>> and_bam = scanBam(and_file, param = ScanBamParam(flag = 
>>>> scanBamFlag(isUnmappedQuery = FALSE), tag = tags))
>>>
>>> *** caught segfault ***
>>> address 0x2b3449beb8cd, cause 'invalid permissions'
>>>
>>> Traceback:
>>> 1: .Call(func, file, index, "rb", NULL, flag, simpleCigar, ...)
>>> 2: .io_bam(.scan_bam, file, index, reverseComplement, tmpl, param = 
>>> param)
>>> 3: scanBam(and_file, param = ScanBamParam(flag = 
>>> scanBamFlag(isUnmappedQuery = FALSE),     tag = tags))
>>> 4: scanBam(and_file, param = ScanBamParam(flag = 
>>> scanBamFlag(isUnmappedQuery = FALSE),     tag = tags))
>>>
>>> This error goes away if we don't include "XS" in tags, also if we use
>>> version 1.0.0 of Rsamtools. Any ideas?
>>>
>>> The sessionInfo() output is below. Thanks in advance!
>>>
>>> --Misha
>>>
>>>> sessionInfo()
>>> R version 2.11.1 (2010-05-31)
>>> x86_64-unknown-linux-gnu
>>>
>>> locale:
>>> [1] C
>>>
>>> attached base packages:
>>> [1] tools     stats     graphics  grDevices utils     datasets  methods
>>> [8] base
>>>
>>> other attached packages:
>>> [1] Rsamtools_1.1.11    Biostrings_2.16.9   GenomicRanges_1.0.7
>>> [4] IRanges_1.6.11      svMisc_0.9-57       JavaGD_0.5-2
>>> [7] rJava_0.8-4
>>>
>>> loaded via a namespace (and not attached):
>>> [1] Biobase_2.8.0
>>>
>>>
>>> On Thu, 12 Aug 2010, Andrew Tikhonov wrote:
>>>
>>>> Dear Biocore Team,
>>>>
>>>>     We've got a problem where 'Rsamtools' produces segfaults and
>>>> core-dumps when reading a .bam file using the "XS" tag. We have a
>>>> faulty .bam and the list or R commands to reproduce it. Could you
>>>> please point us to someone who we may discuss this matter with and,
>>>> if possible, fix the problem.
>>>>
>>>>     Thanks a lot in advance.
>>>>
>>>> Regards,
>>>> Andrew
>>>>
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>>>
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>>
>> -- 
>> Martin Morgan
>> 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
>>